diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 4aaa5cf4..1a78f602 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -122,31 +122,17 @@ jobs: matrix: repo: - afni - - ants - - fsl - - freesurfer - env: - SECRET: "" + # - ants + # - fsl + # - freesurfer + # - mriqc steps: - - name: Get secret for corresponding repo - id: get_secret - run: | - if [ "${{ matrix.repo }}" == "afni" ]; then - SECRET="${{ secrets.AFNI_PAT }}" - elif [ "${{ matrix.repo }}" == "ants" ]; then - SECRET="${{ secrets.ANTS_PAT }}" - elif [ "${{ matrix.repo }}" == "fsl" ]; then - SECRET="${{ secrets.FSL_PAT }}" - elif [ "${{ matrix.repo }}" == "freesurfer" ]; then - SECRET="${{ secrets.FREESURFER_PAT }}" - fi - echo "SECRET=$SECRET" >> $GITHUB_ENV - name: Trigger post-release on downstream repos - if: github.event_name == 'release' && env.SECRET + if: github.event_name == 'release' run: | - curl -XPOST -u "${{ env.SECRET }}" -H "Accept: application/vnd.github.everest-preview+json" \ + curl -XPOST -u "${{ env.POST_RELEASE_PAT }}" -H "Accept: application/vnd.github.everest-preview+json" \ "https://api.github.com/repos/nipype/pydra-${{ matrix.repo }}/dispatches" \ -d '{"event_type": "create-post-release"}' env: - PAT: ${{ env.SECRET }} \ No newline at end of file + PAT: ${{ env.POST_RELEASE_PAT }} diff --git a/example-specs/task/nipype/afni/a_boverlap.yaml b/example-specs/task/nipype/afni/a_boverlap.yaml index d36bb443..4b710470 100644 --- a/example-specs/task/nipype/afni/a_boverlap.yaml +++ b/example-specs/task/nipype/afni/a_boverlap.yaml @@ -142,9 +142,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file_a: + in_file_a: '"functional.nii"' # type=file|default=: input file A - in_file_b: + in_file_b: '"structural.nii"' # type=file|default=: input file B out_file: ' "out.mask_ae_overlap.txt"' # type=file: output file diff --git a/example-specs/task/nipype/afni/afn_ito_nifti.yaml b/example-specs/task/nipype/afni/afn_ito_nifti.yaml index fe003269..ee03b2fd 100644 --- a/example-specs/task/nipype/afni/afn_ito_nifti.yaml +++ b/example-specs/task/nipype/afni/afn_ito_nifti.yaml @@ -137,7 +137,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"afni_output.3D"' # type=file|default=: input file to 3dAFNItoNIFTI out_file: ' "afni_output.nii"' # type=file: output file diff --git a/example-specs/task/nipype/afni/align_epi_anat_py.yaml b/example-specs/task/nipype/afni/align_epi_anat_py.yaml index 50367a88..0bb7bb02 100644 --- a/example-specs/task/nipype/afni/align_epi_anat_py.yaml +++ b/example-specs/task/nipype/afni/align_epi_anat_py.yaml @@ -203,9 +203,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - anat: + anat: '"structural.nii"' # type=file|default=: name of structural dataset - in_file: + in_file: '"functional.nii"' # type=file|default=: EPI dataset to align epi_base: '0' # type=traitcompound|default=None: the epi base used in alignmentshould be one of (0/mean/median/max/subbrick#) diff --git a/example-specs/task/nipype/afni/allineate.yaml b/example-specs/task/nipype/afni/allineate.yaml index ba89bbef..8e6a34cf 100644 --- a/example-specs/task/nipype/afni/allineate.yaml +++ b/example-specs/task/nipype/afni/allineate.yaml @@ -331,12 +331,12 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dAllineate out_file: '"functional_allineate.nii"' # type=file: output image file name # type=file|default=: output file from 3dAllineate - in_matrix: + in_matrix: '"cmatrix.mat"' # type=file|default=: matrix to align input file imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item @@ -349,9 +349,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dAllineate - reference: + reference: '"structural.nii"' # type=file|default=: file to be used as reference, the first volume will be used if not given the reference will be the first volume of in_file. allcostx: '"out.allcostX.txt"' # type=file: Compute and print ALL available cost functionals for the un-warped inputs @@ -367,9 +367,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dAllineate - reference: + reference: '"structural.nii"' # type=file|default=: file to be used as reference, the first volume will be used if not given the reference will be the first volume of in_file. nwarp_fixmot: '["X", "Y"]' # type=list|default=[]: To fix motion along directions. diff --git a/example-specs/task/nipype/afni/auto_tcorrelate.yaml b/example-specs/task/nipype/afni/auto_tcorrelate.yaml index b9d34a84..2033fb58 100644 --- a/example-specs/task/nipype/afni/auto_tcorrelate.yaml +++ b/example-specs/task/nipype/afni/auto_tcorrelate.yaml @@ -151,13 +151,13 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: timeseries x space (volume or surface) file polort: '-1' # type=int|default=0: Remove polynomical trend of order m or -1 for no detrending eta2: 'True' # type=bool|default=False: eta^2 similarity - mask: + mask: '"mask.nii"' # type=file|default=: mask of voxels mask_only_targets: 'True' # type=bool|default=False: use mask only on targets voxels diff --git a/example-specs/task/nipype/afni/auto_tlrc.yaml b/example-specs/task/nipype/afni/auto_tlrc.yaml index 3d30de20..6dec9053 100644 --- a/example-specs/task/nipype/afni/auto_tlrc.yaml +++ b/example-specs/task/nipype/afni/auto_tlrc.yaml @@ -125,7 +125,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: Original anatomical volume (+orig).The skull is removed by this scriptunless instructed otherwise (-no_ss). no_ss: 'True' # type=bool|default=False: Do not strip skull of input data set (because skull has already been removed or because template still has the skull) NOTE: The ``-no_ss`` option is not all that optional. Here is a table of when you should and should not use ``-no_ss`` +------------------+------------+---------------+ | Dataset | Template | +==================+============+===============+ | | w/ skull | wo/ skull | +------------------+------------+---------------+ | WITH skull | ``-no_ss`` | xxx | +------------------+------------+---------------+ | WITHOUT skull | No Cigar | ``-no_ss`` | +------------------+------------+---------------+ Template means: Your template of choice Dset. means: Your anatomical dataset ``-no_ss`` means: Skull stripping should not be attempted on Dset xxx means: Don't put anything, the script will strip Dset No Cigar means: Don't try that combination, it makes no sense. diff --git a/example-specs/task/nipype/afni/autobox.yaml b/example-specs/task/nipype/afni/autobox.yaml index 8b34631c..a290d3f1 100644 --- a/example-specs/task/nipype/afni/autobox.yaml +++ b/example-specs/task/nipype/afni/autobox.yaml @@ -144,7 +144,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: input file padding: '5' # type=int|default=0: Number of extra voxels to pad on each side of box diff --git a/example-specs/task/nipype/afni/automask.yaml b/example-specs/task/nipype/afni/automask.yaml index 4b1d2a0f..6c379956 100644 --- a/example-specs/task/nipype/afni/automask.yaml +++ b/example-specs/task/nipype/afni/automask.yaml @@ -145,7 +145,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dAutomask dilate: '1' # type=int|default=0: dilate the mask outwards diff --git a/example-specs/task/nipype/afni/axialize.yaml b/example-specs/task/nipype/afni/axialize.yaml index 5cef0105..78c9b2de 100644 --- a/example-specs/task/nipype/afni/axialize.yaml +++ b/example-specs/task/nipype/afni/axialize.yaml @@ -139,7 +139,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3daxialize out_file: '"axialized.nii"' # type=file: output file diff --git a/example-specs/task/nipype/afni/bandpass.yaml b/example-specs/task/nipype/afni/bandpass.yaml index cb60f0b7..11c65d8c 100644 --- a/example-specs/task/nipype/afni/bandpass.yaml +++ b/example-specs/task/nipype/afni/bandpass.yaml @@ -169,7 +169,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dBandpass highpass: '0.005' # type=float|default=0.0: highpass diff --git a/example-specs/task/nipype/afni/blur_in_mask.yaml b/example-specs/task/nipype/afni/blur_in_mask.yaml index 6c2e90ac..c6cf5410 100644 --- a/example-specs/task/nipype/afni/blur_in_mask.yaml +++ b/example-specs/task/nipype/afni/blur_in_mask.yaml @@ -148,9 +148,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dSkullStrip - mask: + mask: '"mask.nii"' # type=file|default=: Mask dataset, if desired. Blurring will occur only within the mask. Voxels NOT in the mask will be set to zero in the output. fwhm: '5.0' # type=float|default=0.0: fwhm kernel size diff --git a/example-specs/task/nipype/afni/blur_to_fwhm.yaml b/example-specs/task/nipype/afni/blur_to_fwhm.yaml index aec24f30..ace8e5c3 100644 --- a/example-specs/task/nipype/afni/blur_to_fwhm.yaml +++ b/example-specs/task/nipype/afni/blur_to_fwhm.yaml @@ -142,7 +142,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"epi.nii"' # type=file|default=: The dataset that will be smoothed fwhm: '2.5' # type=float|default=0.0: Blur until the 3D FWHM reaches this value (in mm) diff --git a/example-specs/task/nipype/afni/brick_stat.yaml b/example-specs/task/nipype/afni/brick_stat.yaml index 6c74e1a3..13a936d0 100644 --- a/example-specs/task/nipype/afni/brick_stat.yaml +++ b/example-specs/task/nipype/afni/brick_stat.yaml @@ -138,9 +138,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dmaskave - mask: + mask: '"skeleton_mask.nii.gz"' # type=file|default=: -mask dset = use dset as mask to include/exclude voxels min: 'True' # type=bool|default=False: print the minimum value in dataset diff --git a/example-specs/task/nipype/afni/calc.yaml b/example-specs/task/nipype/afni/calc.yaml index 86bc8152..7b31a119 100644 --- a/example-specs/task/nipype/afni/calc.yaml +++ b/example-specs/task/nipype/afni/calc.yaml @@ -196,9 +196,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file_a: + in_file_a: '"functional.nii"' # type=file|default=: input file to 3dcalc - in_file_b: + in_file_b: '"functional2.nii"' # type=file|default=: operand file to 3dcalc expr: '"a*b"' # type=str|default='': expr @@ -218,7 +218,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file_a: + in_file_a: '"functional.nii"' # type=file|default=: input file to 3dcalc expr: '"1"' # type=str|default='': expr diff --git a/example-specs/task/nipype/afni/cat.yaml b/example-specs/task/nipype/afni/cat.yaml index 31eb9a2a..74983e72 100644 --- a/example-specs/task/nipype/afni/cat.yaml +++ b/example-specs/task/nipype/afni/cat.yaml @@ -155,7 +155,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. sel: '"''[0,2]''"' # type=str|default='': Apply the same column/row selection string to all filenames on the command line. - in_files: + in_files: '["f1.1D", "f2.1D"]' # type=list|default=[]: out_file: '"catout.1d"' # type=file: output file diff --git a/example-specs/task/nipype/afni/center_mass.yaml b/example-specs/task/nipype/afni/center_mass.yaml index a6981eb8..67e048ae 100644 --- a/example-specs/task/nipype/afni/center_mass.yaml +++ b/example-specs/task/nipype/afni/center_mass.yaml @@ -149,7 +149,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: input file to 3dCM cm_file: '"cm.txt"' # type=file: file with the center of mass coordinates diff --git a/example-specs/task/nipype/afni/clip_level.yaml b/example-specs/task/nipype/afni/clip_level.yaml index bc1eb0b0..01699314 100644 --- a/example-specs/task/nipype/afni/clip_level.yaml +++ b/example-specs/task/nipype/afni/clip_level.yaml @@ -122,7 +122,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"anatomical.nii"' # type=file|default=: input file to 3dClipLevel imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/afni/convert_dset.yaml b/example-specs/task/nipype/afni/convert_dset.yaml index 70b3be29..b08ff9ad 100644 --- a/example-specs/task/nipype/afni/convert_dset.yaml +++ b/example-specs/task/nipype/afni/convert_dset.yaml @@ -133,7 +133,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"lh.pial_converted.gii"' # type=file|default=: input file to ConvertDset out_type: '"niml_asc"' # type=enum|default='niml'|allowed['1D','1Dp','1Dpt','gii','gii_asc','gii_b64','gii_b64gz','niml','niml_asc','niml_bi']: output type diff --git a/example-specs/task/nipype/afni/copy.yaml b/example-specs/task/nipype/afni/copy.yaml index 94c744c1..ed4e6da6 100644 --- a/example-specs/task/nipype/afni/copy.yaml +++ b/example-specs/task/nipype/afni/copy.yaml @@ -210,7 +210,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dcopy imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/afni/deconvolve.yaml b/example-specs/task/nipype/afni/deconvolve.yaml index b30709b9..06fadcac 100644 --- a/example-specs/task/nipype/afni/deconvolve.yaml +++ b/example-specs/task/nipype/afni/deconvolve.yaml @@ -248,7 +248,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["functional.nii", "functional2.nii"]' # type=inputmultiobject|default=[]: filenames of 3D+time input datasets. More than one filename can be given and the datasets will be auto-catenated in time. You can input a 1D time series file here, but the time axis should run along the ROW direction, not the COLUMN direction as in the 'input1D' option. out_file: '"output.nii"' # type=file: output statistics file diff --git a/example-specs/task/nipype/afni/degree_centrality.yaml b/example-specs/task/nipype/afni/degree_centrality.yaml index f187adce..a72b78c1 100644 --- a/example-specs/task/nipype/afni/degree_centrality.yaml +++ b/example-specs/task/nipype/afni/degree_centrality.yaml @@ -155,9 +155,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dDegreeCentrality - mask: + mask: '"mask.nii"' # type=file|default=: mask file to mask input data sparsity: '1 # keep the top one percent of connections' # type=float|default=0.0: only take the top percent of connections diff --git a/example-specs/task/nipype/afni/despike.yaml b/example-specs/task/nipype/afni/despike.yaml index 23855511..23cec1f6 100644 --- a/example-specs/task/nipype/afni/despike.yaml +++ b/example-specs/task/nipype/afni/despike.yaml @@ -124,7 +124,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dDespike imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/afni/detrend.yaml b/example-specs/task/nipype/afni/detrend.yaml index d4089ebb..6b023d2e 100644 --- a/example-specs/task/nipype/afni/detrend.yaml +++ b/example-specs/task/nipype/afni/detrend.yaml @@ -131,7 +131,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dDetrend args: '"-polort 2"' # type=str|default='': Additional parameters to the command diff --git a/example-specs/task/nipype/afni/dot.yaml b/example-specs/task/nipype/afni/dot.yaml index 7c21b4fd..eb94d2e9 100644 --- a/example-specs/task/nipype/afni/dot.yaml +++ b/example-specs/task/nipype/afni/dot.yaml @@ -161,7 +161,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["functional.nii[0]", "structural.nii"]' # type=list|default=[]: list of input files, possibly with subbrick selectors dodice: 'True' # type=bool|default=False: Return the Dice coefficient (the Sorensen-Dice index). diff --git a/example-specs/task/nipype/afni/ecm.yaml b/example-specs/task/nipype/afni/ecm.yaml index d813de93..ef7a5767 100644 --- a/example-specs/task/nipype/afni/ecm.yaml +++ b/example-specs/task/nipype/afni/ecm.yaml @@ -163,9 +163,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dECM - mask: + mask: '"mask.nii"' # type=file|default=: mask file to mask input data sparsity: '0.1 # keep top 0.1% of connections' # type=float|default=0.0: only take the top percent of connections diff --git a/example-specs/task/nipype/afni/edge_3.yaml b/example-specs/task/nipype/afni/edge_3.yaml index f5a6aa1f..7d52d966 100644 --- a/example-specs/task/nipype/afni/edge_3.yaml +++ b/example-specs/task/nipype/afni/edge_3.yaml @@ -144,7 +144,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dedge3 out_file: '"edges.nii"' # type=file: output file diff --git a/example-specs/task/nipype/afni/eval.yaml b/example-specs/task/nipype/afni/eval.yaml index 2396f10e..acd88eaa 100644 --- a/example-specs/task/nipype/afni/eval.yaml +++ b/example-specs/task/nipype/afni/eval.yaml @@ -160,9 +160,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file_a: + in_file_a: '"seed.1D"' # type=file|default=: input file to 1deval - in_file_b: + in_file_b: '"resp.1D"' # type=file|default=: operand file to 1deval expr: '"a*b"' # type=str|default='': expr diff --git a/example-specs/task/nipype/afni/fim.yaml b/example-specs/task/nipype/afni/fim.yaml index 53c43538..076e5cc3 100644 --- a/example-specs/task/nipype/afni/fim.yaml +++ b/example-specs/task/nipype/afni/fim.yaml @@ -146,9 +146,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dfim+ - ideal_file: + ideal_file: '"seed.1D"' # type=file|default=: ideal time series file name out_file: '"functional_corr.nii"' # type=file: output file diff --git a/example-specs/task/nipype/afni/fourier.yaml b/example-specs/task/nipype/afni/fourier.yaml index d5afa6f1..029f08a6 100644 --- a/example-specs/task/nipype/afni/fourier.yaml +++ b/example-specs/task/nipype/afni/fourier.yaml @@ -140,7 +140,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dFourier retrend: 'True' # type=bool|default=False: Any mean and linear trend are removed before filtering. This will restore the trend after filtering. diff --git a/example-specs/task/nipype/afni/fwh_mx.yaml b/example-specs/task/nipype/afni/fwh_mx.yaml index f429f2df..34d36603 100644 --- a/example-specs/task/nipype/afni/fwh_mx.yaml +++ b/example-specs/task/nipype/afni/fwh_mx.yaml @@ -245,7 +245,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input dataset imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/afni/gcor.yaml b/example-specs/task/nipype/afni/gcor.yaml index ec32ac93..451c2d5e 100644 --- a/example-specs/task/nipype/afni/gcor.yaml +++ b/example-specs/task/nipype/afni/gcor.yaml @@ -127,7 +127,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: input dataset to compute the GCOR over nfirst: '4' # type=int|default=0: specify number of initial TRs to ignore diff --git a/example-specs/task/nipype/afni/hist.yaml b/example-specs/task/nipype/afni/hist.yaml index 88a41000..86e03533 100644 --- a/example-specs/task/nipype/afni/hist.yaml +++ b/example-specs/task/nipype/afni/hist.yaml @@ -144,7 +144,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dHist imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/afni/lfcd.yaml b/example-specs/task/nipype/afni/lfcd.yaml index 61155920..92945608 100644 --- a/example-specs/task/nipype/afni/lfcd.yaml +++ b/example-specs/task/nipype/afni/lfcd.yaml @@ -146,9 +146,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dLFCD - mask: + mask: '"mask.nii"' # type=file|default=: mask file to mask input data thresh: '0.8 # keep all connections with corr >= 0.8' # type=float|default=0.0: threshold to exclude connections where corr <= thresh diff --git a/example-specs/task/nipype/afni/local_bistat.yaml b/example-specs/task/nipype/afni/local_bistat.yaml index eba6cc0b..97b8f92c 100644 --- a/example-specs/task/nipype/afni/local_bistat.yaml +++ b/example-specs/task/nipype/afni/local_bistat.yaml @@ -155,9 +155,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file1: + in_file1: '"functional.nii"' # type=file|default=: Filename of the first image - in_file2: + in_file2: '"structural.nii"' # type=file|default=: Filename of the second image neighborhood: ("SPHERE", 1.2) # type=traitcompound|default=None: The region around each voxel that will be extracted for the statistics calculation. Possible regions are: 'SPHERE', 'RHDD' (rhombic dodecahedron), 'TOHD' (truncated octahedron) with a given radius in mm or 'RECT' (rectangular block) with dimensions to specify in mm. diff --git a/example-specs/task/nipype/afni/localstat.yaml b/example-specs/task/nipype/afni/localstat.yaml index 60cabd9b..dba6496b 100644 --- a/example-specs/task/nipype/afni/localstat.yaml +++ b/example-specs/task/nipype/afni/localstat.yaml @@ -164,9 +164,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input dataset - mask_file: + mask_file: '"skeleton_mask.nii.gz"' # type=file|default=: Mask image file name. Voxels NOT in the mask will not be used in the neighborhood of any voxel. Also, a voxel NOT in the mask will have its statistic(s) computed as zero (0) unless the parameter 'nonmask' is set to true. neighborhood: ("SPHERE", 45) # type=traitcompound|default=None: The region around each voxel that will be extracted for the statistics calculation. Possible regions are: 'SPHERE', 'RHDD' (rhombic dodecahedron), 'TOHD' (truncated octahedron) with a given radius in mm or 'RECT' (rectangular block) with dimensions to specify in mm. diff --git a/example-specs/task/nipype/afni/mask_tool.yaml b/example-specs/task/nipype/afni/mask_tool.yaml index e53b9679..a61da219 100644 --- a/example-specs/task/nipype/afni/mask_tool.yaml +++ b/example-specs/task/nipype/afni/mask_tool.yaml @@ -147,7 +147,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=inputmultiobject|default=[]: input file or files to 3dmask_tool outputtype: '"NIFTI"' # type=enum|default='AFNI'|allowed['AFNI','NIFTI','NIFTI_GZ']: AFNI output filetype diff --git a/example-specs/task/nipype/afni/maskave.yaml b/example-specs/task/nipype/afni/maskave.yaml index 4cdfab64..cb035e58 100644 --- a/example-specs/task/nipype/afni/maskave.yaml +++ b/example-specs/task/nipype/afni/maskave.yaml @@ -137,9 +137,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dmaskave - mask: + mask: '"seed_mask.nii"' # type=file|default=: matrix to align input file quiet: 'True' # type=bool|default=False: matrix to align input file diff --git a/example-specs/task/nipype/afni/means.yaml b/example-specs/task/nipype/afni/means.yaml index e0d94cbf..eb8748eb 100644 --- a/example-specs/task/nipype/afni/means.yaml +++ b/example-specs/task/nipype/afni/means.yaml @@ -187,9 +187,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file_a: + in_file_a: '"im1.nii"' # type=file|default=: input file to 3dMean - in_file_b: + in_file_b: '"im2.nii"' # type=file|default=: another input file to 3dMean out_file: ' "output.nii"' # type=file: output file @@ -205,7 +205,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file_a: + in_file_a: '"im1.nii"' # type=file|default=: input file to 3dMean out_file: ' "output.nii"' # type=file: output file diff --git a/example-specs/task/nipype/afni/merge.yaml b/example-specs/task/nipype/afni/merge.yaml index 64e45124..807163d2 100644 --- a/example-specs/task/nipype/afni/merge.yaml +++ b/example-specs/task/nipype/afni/merge.yaml @@ -138,7 +138,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["functional.nii", "functional2.nii"]' # type=inputmultiobject|default=[]: blurfwhm: '4' # type=int|default=0: FWHM blur value (mm) diff --git a/example-specs/task/nipype/afni/net_corr.yaml b/example-specs/task/nipype/afni/net_corr.yaml index afbce2ba..fa1c7e32 100644 --- a/example-specs/task/nipype/afni/net_corr.yaml +++ b/example-specs/task/nipype/afni/net_corr.yaml @@ -178,11 +178,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input time series file (4D data set) - mask: + mask: '"mask.nii"' # type=file|default=: can include a whole brain mask within which to calculate correlation. Otherwise, data should be masked already - in_rois: + in_rois: '"maps.nii"' # type=file|default=: input set of ROIs, each labelled with distinct integers ts_wb_corr: 'True' # type=bool|default=False: switch to create a set of whole brain correlation maps. Performs whole brain correlation for each ROI's average time series; this will automatically create a directory for each network that contains the set of whole brain correlation maps (Pearson 'r's). The directories are labelled as above for '-ts_indiv' Within each directory, the files are labelled WB_CORR_ROI_001+orig, WB_CORR_ROI_002+orig, etc., with the numbers given by the actual ROI integer labels diff --git a/example-specs/task/nipype/afni/notes.yaml b/example-specs/task/nipype/afni/notes.yaml index 12862ecc..379c9378 100644 --- a/example-specs/task/nipype/afni/notes.yaml +++ b/example-specs/task/nipype/afni/notes.yaml @@ -140,7 +140,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.HEAD"' # type=file|default=: input file to 3dNotes add: '"This note is added."' # type=str|default='': note to add diff --git a/example-specs/task/nipype/afni/nwarp_adjust.yaml b/example-specs/task/nipype/afni/nwarp_adjust.yaml index 74eb8757..94fc924e 100644 --- a/example-specs/task/nipype/afni/nwarp_adjust.yaml +++ b/example-specs/task/nipype/afni/nwarp_adjust.yaml @@ -133,7 +133,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - warps: + warps: '["func2anat_InverseWarp.nii.gz", "func2anat_InverseWarp.nii.gz", "func2anat_InverseWarp.nii.gz", "func2anat_InverseWarp.nii.gz", "func2anat_InverseWarp.nii.gz"]' # type=inputmultiobject|default=[]: List of input 3D warp datasets imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/afni/nwarp_apply.yaml b/example-specs/task/nipype/afni/nwarp_apply.yaml index fee70bec..0207690d 100644 --- a/example-specs/task/nipype/afni/nwarp_apply.yaml +++ b/example-specs/task/nipype/afni/nwarp_apply.yaml @@ -146,7 +146,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. in_file: '"Fred+orig"' # type=traitcompound|default=None: the name of the dataset to be warped can be multiple datasets - master: + master: '"NWARP"' # type=file|default=: the name of the master dataset, which defines the output grid warp: '"''Fred_WARP+tlrc Fred.Xaff12.1D''"' # type=string|default='': the name of the warp dataset. multiple warps can be concatenated (make sure they exist) diff --git a/example-specs/task/nipype/afni/one_d_tool_py.yaml b/example-specs/task/nipype/afni/one_d_tool_py.yaml index bfd7bdeb..da52c7c3 100644 --- a/example-specs/task/nipype/afni/one_d_tool_py.yaml +++ b/example-specs/task/nipype/afni/one_d_tool_py.yaml @@ -150,7 +150,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"f1.1D"' # type=file|default=: input file to OneDTool set_nruns: '3' # type=int|default=0: treat the input data as if it has nruns diff --git a/example-specs/task/nipype/afni/outlier_count.yaml b/example-specs/task/nipype/afni/outlier_count.yaml index 0e74700f..36bfb07f 100644 --- a/example-specs/task/nipype/afni/outlier_count.yaml +++ b/example-specs/task/nipype/afni/outlier_count.yaml @@ -147,7 +147,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input dataset imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/afni/quality_index.yaml b/example-specs/task/nipype/afni/quality_index.yaml index 5380f415..d79863fe 100644 --- a/example-specs/task/nipype/afni/quality_index.yaml +++ b/example-specs/task/nipype/afni/quality_index.yaml @@ -140,7 +140,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input dataset imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/afni/qwarp.yaml b/example-specs/task/nipype/afni/qwarp.yaml index 0ed6ee9d..11c539b2 100644 --- a/example-specs/task/nipype/afni/qwarp.yaml +++ b/example-specs/task/nipype/afni/qwarp.yaml @@ -482,11 +482,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"sub-01_dir-LR_epi.nii.gz"' # type=file|default=: Source image (opposite phase encoding direction than base image). nopadWARP: 'True' # type=bool|default=False: If for some reason you require the warp volume tomatch the base volume, then use this option to have the outputWARP dataset(s) truncated. - base_file: + base_file: '"sub-01_dir-RL_epi.nii.gz"' # type=file|default=: Base image (opposite phase encoding direction than source image). plusminus: 'True' # type=bool|default=False: Normally, the warp displacements dis(x) are defined to match base(x) to source(x+dis(x)). With this option, the match is between base(x-dis(x)) and source(x+dis(x)) -- the two images 'meet in the middle'. * One goal is to mimic the warping done to MRI EPI data by field inhomogeneities, when registering between a 'blip up' and a 'blip down' down volume, which will have opposite distortions. * Define Wp(x) = x+dis(x) and Wm(x) = x-dis(x). Then since base(Wm(x)) matches source(Wp(x)), by substituting INV(Wm(x)) wherever we see x, we have base(x) matches source(Wp(INV(Wm(x)))); that is, the warp V(x) that one would get from the 'usual' way of running 3dQwarp is V(x) = Wp(INV(Wm(x))). * Conversely, we can calculate Wp(x) in terms of V(x) as follows: If V(x) = x + dv(x), define Vh(x) = x + dv(x)/2; then Wp(x) = V(INV(Vh(x))) * With the above formulas, it is possible to compute Wp(x) from V(x) and vice-versa, using program 3dNwarpCalc. The requisite commands are left as an exercise for the aspiring AFNI Jedi Master. * You can use the semi-secret '-pmBASE' option to get the V(x) warp and the source dataset warped to base space, in addition to the Wp(x) '_PLUS' and Wm(x) '_MINUS' warps. * Alas: -plusminus does not work with -duplo or -allineate :-( * However, you can use -iniwarp with -plusminus :-) * The outputs have _PLUS (from the source dataset) and _MINUS (from the base dataset) in their filenames, in addition to the prefix. The -iwarp option, if present, will be ignored. @@ -501,9 +501,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: Source image (opposite phase encoding direction than base image). - base_file: + base_file: '"mni.nii"' # type=file|default=: Base image (opposite phase encoding direction than source image). resample: 'True' # type=bool|default=False: This option simply resamples the source dataset to match the base dataset grid. You can use this if the two datasets overlap well (as seen in the AFNI GUI), but are not on the same 3D grid. * If they don't overlap well, allineate them first * The reampling here is done with the 'wsinc5' method, which has very little blurring artifact. * If the base and source datasets ARE on the same 3D grid, then the -resample option will be ignored. * You CAN use -resample with these 3dQwarp options: -plusminus -inilev -iniwarp -duplo @@ -518,9 +518,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: Source image (opposite phase encoding direction than base image). - base_file: + base_file: '"epi.nii"' # type=file|default=: Base image (opposite phase encoding direction than source image). out_file: '"anatSSQ.nii.gz"' # type=file|default=: Sets the prefix/suffix for the output datasets. * The source dataset is warped to match the base and gets prefix 'ppp'. (Except if '-plusminus' is used * The final interpolation to this output dataset is done using the 'wsinc5' method. See the output of 3dAllineate -HELP (in the "Modifying '-final wsinc5'" section) for the lengthy technical details. * The 3D warp used is saved in a dataset with prefix 'ppp_WARP' -- this dataset can be used with 3dNwarpApply and 3dNwarpCat, for example. * To be clear, this is the warp from source dataset coordinates to base dataset coordinates, where the values at each base grid point are the xyz displacements needed to move that grid point's xyz values to the corresponding xyz values in the source dataset: base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z) Another way to think of this warp is that it 'pulls' values back from source space to base space. * 3dNwarpApply would use 'ppp_WARP' to transform datasets aligned with the source dataset to be aligned with the base dataset. **If you do NOT want this warp saved, use the option '-nowarp'**. (However, this warp is usually the most valuable possible output!) * If you want to calculate and save the inverse 3D warp, use the option '-iwarp'. This inverse warp will then be saved in a dataset with prefix 'ppp_WARPINV'. * This inverse warp could be used to transform data from base space to source space, if you need to do such an operation. * You can easily compute the inverse later, say by a command like 3dNwarpCat -prefix Z_WARPINV 'INV(Z_WARP+tlrc)' or the inverse can be computed as needed in 3dNwarpApply, like 3dNwarpApply -nwarp 'INV(Z_WARP+tlrc)' -source Dataset.nii ... @@ -545,9 +545,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: Source image (opposite phase encoding direction than base image). - base_file: + base_file: '"mni.nii"' # type=file|default=: Base image (opposite phase encoding direction than source image). duplo: 'True' # type=bool|default=False: Start off with 1/2 scale versions of the volumes," for getting a speedy coarse first alignment." * Then scales back up to register the full volumes." The goal is greater speed, and it seems to help this" positively piggish program to be more expeditious." * However, accuracy is somewhat lower with '-duplo'," for reasons that currently elude Zhark; for this reason," the Emperor does not usually use '-duplo'. @@ -564,9 +564,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: Source image (opposite phase encoding direction than base image). - base_file: + base_file: '"mni.nii"' # type=file|default=: Base image (opposite phase encoding direction than source image). duplo: 'True' # type=bool|default=False: Start off with 1/2 scale versions of the volumes," for getting a speedy coarse first alignment." * Then scales back up to register the full volumes." The goal is greater speed, and it seems to help this" positively piggish program to be more expeditious." * However, accuracy is somewhat lower with '-duplo'," for reasons that currently elude Zhark; for this reason," the Emperor does not usually use '-duplo'. @@ -587,9 +587,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: Source image (opposite phase encoding direction than base image). - base_file: + base_file: '"mni.nii"' # type=file|default=: Base image (opposite phase encoding direction than source image). blur: '[0,2]' # type=list|default=[]: Gaussian blur the input images by 'bb' (FWHM) voxels before doing the alignment (the output dataset will not be blurred). The default is 2.345 (for no good reason). * Optionally, you can provide 2 values for 'bb', and then the first one is applied to the base volume, the second to the source volume. e.g., '-blur 0 3' to skip blurring the base image (if the base is a blurry template, for example). * A negative blur radius means to use 3D median filtering, rather than Gaussian blurring. This type of filtering will better preserve edges, which can be important in alignment. * If the base is a template volume that is already blurry, you probably don't want to blur it again, but blurring the source volume a little is probably a good idea, to help the program avoid trying to match tiny features. * Note that -duplo will blur the volumes some extra amount for the initial small-scale warping, to make that phase of the program converge more rapidly. @@ -597,7 +597,7 @@ doctests: # type=file|default=: Sets the prefix/suffix for the output datasets. * The source dataset is warped to match the base and gets prefix 'ppp'. (Except if '-plusminus' is used * The final interpolation to this output dataset is done using the 'wsinc5' method. See the output of 3dAllineate -HELP (in the "Modifying '-final wsinc5'" section) for the lengthy technical details. * The 3D warp used is saved in a dataset with prefix 'ppp_WARP' -- this dataset can be used with 3dNwarpApply and 3dNwarpCat, for example. * To be clear, this is the warp from source dataset coordinates to base dataset coordinates, where the values at each base grid point are the xyz displacements needed to move that grid point's xyz values to the corresponding xyz values in the source dataset: base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z) Another way to think of this warp is that it 'pulls' values back from source space to base space. * 3dNwarpApply would use 'ppp_WARP' to transform datasets aligned with the source dataset to be aligned with the base dataset. **If you do NOT want this warp saved, use the option '-nowarp'**. (However, this warp is usually the most valuable possible output!) * If you want to calculate and save the inverse 3D warp, use the option '-iwarp'. This inverse warp will then be saved in a dataset with prefix 'ppp_WARPINV'. * This inverse warp could be used to transform data from base space to source space, if you need to do such an operation. * You can easily compute the inverse later, say by a command like 3dNwarpCat -prefix Z_WARPINV 'INV(Z_WARP+tlrc)' or the inverse can be computed as needed in 3dNwarpApply, like 3dNwarpApply -nwarp 'INV(Z_WARP+tlrc)' -source Dataset.nii ... inilev: '7' # type=int|default=0: The initial refinement 'level' at which to start. * Usually used with -iniwarp; CANNOT be used with -duplo. * The combination of -inilev and -iniwarp lets you take the results of a previous 3dQwarp run and refine them further: Note that the source dataset in the second run is the SAME as in the first run. If you don't see why this is necessary, then you probably need to seek help from an AFNI guru. - iniwarp: + iniwarp: '["Q25_warp+tlrc.HEAD"]' # type=list|default=[]: A dataset with an initial nonlinear warp to use. * If this option is not used, the initial warp is the identity. * You can specify a catenation of warps (in quotes) here, as in program 3dNwarpApply. * As a special case, if you just input an affine matrix in a .1D file, that will work also -- it is treated as giving the initial warp via the string "IDENT(base_dataset) matrix_file.aff12.1D". * You CANNOT use this option with -duplo !! * -iniwarp is usually used with -inilev to re-start 3dQwarp from a previous stopping point. imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item @@ -610,9 +610,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: Source image (opposite phase encoding direction than base image). - base_file: + base_file: '"mni.nii"' # type=file|default=: Base image (opposite phase encoding direction than source image). allineate: 'True' # type=bool|default=False: This option will make 3dQwarp run 3dAllineate first, to align the source dataset to the base with an affine transformation. It will then use that alignment as a starting point for the nonlinear warping. diff --git a/example-specs/task/nipype/afni/qwarp_plus_minus.yaml b/example-specs/task/nipype/afni/qwarp_plus_minus.yaml index 47f3e26b..8e5bf757 100644 --- a/example-specs/task/nipype/afni/qwarp_plus_minus.yaml +++ b/example-specs/task/nipype/afni/qwarp_plus_minus.yaml @@ -244,11 +244,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"sub-01_dir-LR_epi.nii.gz"' # type=file|default=: Source image (opposite phase encoding direction than base image). nopadWARP: 'True' # type=bool|default=False: If for some reason you require the warp volume tomatch the base volume, then use this option to have the outputWARP dataset(s) truncated. - base_file: + base_file: '"sub-01_dir-RL_epi.nii.gz"' # type=file|default=: Base image (opposite phase encoding direction than source image). imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/afni/re_ho.yaml b/example-specs/task/nipype/afni/re_ho.yaml index e12c8d8c..ccc8263d 100644 --- a/example-specs/task/nipype/afni/re_ho.yaml +++ b/example-specs/task/nipype/afni/re_ho.yaml @@ -148,7 +148,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input dataset out_file: '"reho.nii.gz"' # type=file: Voxelwise regional homogeneity map diff --git a/example-specs/task/nipype/afni/refit.yaml b/example-specs/task/nipype/afni/refit.yaml index 94ccb95a..7e544735 100644 --- a/example-specs/task/nipype/afni/refit.yaml +++ b/example-specs/task/nipype/afni/refit.yaml @@ -179,7 +179,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: input file to 3drefit deoblique: 'True' # type=bool|default=False: replace current transformation matrix with cardinal matrix @@ -194,7 +194,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: input file to 3drefit atrfloat: ("IJK_TO_DICOM_REAL", "'1 0.2 0 0 -0.2 1 0 0 0 0 1 0'") # type=tuple|default=('', ''): Create or modify floating point attributes. The input values may be specified as a single string in quotes or as a 1D filename or string, example '1 0.2 0 0 -0.2 1 0 0 0 0 1 0' or flipZ.1D or '1D:1,0.2,2@0,-0.2,1,2@0,2@0,1,0' diff --git a/example-specs/task/nipype/afni/remlfit.yaml b/example-specs/task/nipype/afni/remlfit.yaml index 64cc639b..fc213b35 100644 --- a/example-specs/task/nipype/afni/remlfit.yaml +++ b/example-specs/task/nipype/afni/remlfit.yaml @@ -304,12 +304,12 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["functional.nii", "functional2.nii"]' # type=inputmultiobject|default=[]: Read time series dataset out_file: '"output.nii"' # type=file: dataset for beta + statistics from the REML estimation (if generated # type=file|default=: output dataset for beta + statistics from the REML estimation; also contains the results of any GLT analysis requested in the Deconvolve setup, similar to the 'bucket' output from Deconvolve. This dataset does NOT get the betas (or statistics) of those regressors marked as 'baseline' in the matrix file. - matrix: + matrix: '"output.1D"' # type=file|default=: the design matrix file, which should have been output from Deconvolve via the 'x1D' option gltsym: '[("SYM: +Lab1 -Lab2", "TestSYM"), ("timeseries.txt", "TestFile")]' # type=list|default=[]: read a symbolic GLT from input file and associate it with a label. As in Deconvolve, you can also use the 'SYM:' method to provide the definition of the GLT directly as a string (e.g., with 'SYM: +Label1 -Label2'). Unlike Deconvolve, you MUST specify 'SYM: ' if providing the GLT directly as a string instead of from a file diff --git a/example-specs/task/nipype/afni/resample.yaml b/example-specs/task/nipype/afni/resample.yaml index 8cbb778e..802b962a 100644 --- a/example-specs/task/nipype/afni/resample.yaml +++ b/example-specs/task/nipype/afni/resample.yaml @@ -140,7 +140,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dresample orientation: '"RPI"' # type=str|default='': new orientation code diff --git a/example-specs/task/nipype/afni/retroicor.yaml b/example-specs/task/nipype/afni/retroicor.yaml index b724cc68..9b2bd338 100644 --- a/example-specs/task/nipype/afni/retroicor.yaml +++ b/example-specs/task/nipype/afni/retroicor.yaml @@ -168,11 +168,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dretroicor - card: + card: '"mask.1D"' # type=file|default=: 1D cardiac data file for cardiac correction - resp: + resp: '"resp.1D"' # type=file|default=: 1D respiratory waveform data for correction outputtype: '"NIFTI"' # type=enum|default='AFNI'|allowed['AFNI','NIFTI','NIFTI_GZ']: AFNI output filetype diff --git a/example-specs/task/nipype/afni/roi_stats.yaml b/example-specs/task/nipype/afni/roi_stats.yaml index 3360e295..9cc2cfea 100644 --- a/example-specs/task/nipype/afni/roi_stats.yaml +++ b/example-specs/task/nipype/afni/roi_stats.yaml @@ -161,9 +161,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input dataset - mask_file: + mask_file: '"skeleton_mask.nii.gz"' # type=file|default=: input mask stat: '["mean", "median", "voxels"]' # type=inputmultiobject|default=[]: Statistics to compute. Options include: * mean = Compute the mean using only non_zero voxels. Implies the opposite for the mean computed by default. * median = Compute the median of nonzero voxels * mode = Compute the mode of nonzero voxels. (integral valued sets only) * minmax = Compute the min/max of nonzero voxels * sum = Compute the sum using only nonzero voxels. * voxels = Compute the number of nonzero voxels * sigma = Compute the standard deviation of nonzero voxels Statistics that include zero-valued voxels: * zerominmax = Compute the min/max of all voxels. * zerosigma = Compute the standard deviation of all voxels. * zeromedian = Compute the median of all voxels. * zeromode = Compute the mode of all voxels. * summary = Only output a summary line with the grand mean across all briks in the input dataset. This option cannot be used with nomeanout. More that one option can be specified. diff --git a/example-specs/task/nipype/afni/seg.yaml b/example-specs/task/nipype/afni/seg.yaml index 8704d95a..6b900b57 100644 --- a/example-specs/task/nipype/afni/seg.yaml +++ b/example-specs/task/nipype/afni/seg.yaml @@ -138,7 +138,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: ANAT is the volume to segment mask: '"AUTO"' # type=traitcompound|default=None: only non-zero voxels in mask are analyzed. mask can either be a dataset or the string "AUTO" which would use AFNI's automask function to create the mask. diff --git a/example-specs/task/nipype/afni/skull_strip.yaml b/example-specs/task/nipype/afni/skull_strip.yaml index 6b1993e8..1da38ac7 100644 --- a/example-specs/task/nipype/afni/skull_strip.yaml +++ b/example-specs/task/nipype/afni/skull_strip.yaml @@ -129,7 +129,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dSkullStrip args: '"-o_ply"' # type=str|default='': Additional parameters to the command diff --git a/example-specs/task/nipype/afni/synthesize.yaml b/example-specs/task/nipype/afni/synthesize.yaml index 246cc1e0..fea928ec 100644 --- a/example-specs/task/nipype/afni/synthesize.yaml +++ b/example-specs/task/nipype/afni/synthesize.yaml @@ -144,9 +144,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - cbucket: + cbucket: '"functional.nii"' # type=file|default=: Read the dataset output from 3dDeconvolve via the '-cbucket' option. - matrix: + matrix: '"output.1D"' # type=file|default=: Read the matrix output from 3dDeconvolve via the '-x1D' option. select: '["baseline"]' # type=list|default=[]: A list of selected columns from the matrix (and the corresponding coefficient sub-bricks from the cbucket). Valid types include 'baseline', 'polort', 'allfunc', 'allstim', 'all', Can also provide 'something' where something matches a stim_label from 3dDeconvolve, and 'digits' where digits are the numbers of the select matrix columns by numbers (starting at 0), or number ranges of the form '3..7' and '3-7'. diff --git a/example-specs/task/nipype/afni/t_cat.yaml b/example-specs/task/nipype/afni/t_cat.yaml index c15b03d9..f281668f 100644 --- a/example-specs/task/nipype/afni/t_cat.yaml +++ b/example-specs/task/nipype/afni/t_cat.yaml @@ -138,7 +138,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["functional.nii", "functional2.nii"]' # type=inputmultiobject|default=[]: input file to 3dTcat out_file: '"functional_tcat.nii"' # type=file: output file diff --git a/example-specs/task/nipype/afni/t_corr_1d.yaml b/example-specs/task/nipype/afni/t_corr_1d.yaml index 1e91c8c8..20713833 100644 --- a/example-specs/task/nipype/afni/t_corr_1d.yaml +++ b/example-specs/task/nipype/afni/t_corr_1d.yaml @@ -138,9 +138,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - xset: + xset: '"u_rc1s1_Template.nii"' # type=file|default=: 3d+time dataset input - y_1d: + y_1d: '"seed.1D"' # type=file|default=: 1D time series file input imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/afni/t_corr_map.yaml b/example-specs/task/nipype/afni/t_corr_map.yaml index bafdfb92..8fb389b8 100644 --- a/example-specs/task/nipype/afni/t_corr_map.yaml +++ b/example-specs/task/nipype/afni/t_corr_map.yaml @@ -270,9 +270,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: - mask: + mask: '"mask.nii"' # type=file|default=: imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/afni/t_correlate.yaml b/example-specs/task/nipype/afni/t_correlate.yaml index f1be2e6c..7067997b 100644 --- a/example-specs/task/nipype/afni/t_correlate.yaml +++ b/example-specs/task/nipype/afni/t_correlate.yaml @@ -146,9 +146,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - xset: + xset: '"u_rc1s1_Template.nii"' # type=file|default=: input xset - yset: + yset: '"u_rc1s2_Template.nii"' # type=file|default=: input yset out_file: '"functional_tcorrelate.nii.gz"' # type=file: output file diff --git a/example-specs/task/nipype/afni/t_norm.yaml b/example-specs/task/nipype/afni/t_norm.yaml index 6c7d143a..f78630fc 100644 --- a/example-specs/task/nipype/afni/t_norm.yaml +++ b/example-specs/task/nipype/afni/t_norm.yaml @@ -144,7 +144,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dTNorm norm2: 'True' # type=bool|default=False: L2 normalize (sum of squares = 1) [DEFAULT] diff --git a/example-specs/task/nipype/afni/t_project.yaml b/example-specs/task/nipype/afni/t_project.yaml index 31d2bb7c..50c16683 100644 --- a/example-specs/task/nipype/afni/t_project.yaml +++ b/example-specs/task/nipype/afni/t_project.yaml @@ -187,7 +187,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dTproject bandpass: (0.00667, 99999) # type=tuple|default=(0.0, 0.0): Remove all frequencies EXCEPT those in the range diff --git a/example-specs/task/nipype/afni/t_shift.yaml b/example-specs/task/nipype/afni/t_shift.yaml index 4201d06d..eeb1f7d1 100644 --- a/example-specs/task/nipype/afni/t_shift.yaml +++ b/example-specs/task/nipype/afni/t_shift.yaml @@ -323,7 +323,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dTshift tzero: '0.0' # type=float|default=0.0: align each slice to given time offset @@ -355,7 +355,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dTshift tzero: '0.0' # type=float|default=0.0: align each slice to given time offset @@ -374,7 +374,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dTshift tzero: '0.0' # type=float|default=0.0: align each slice to given time offset @@ -393,7 +393,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dTshift tzero: '0.0' # type=float|default=0.0: align each slice to given time offset diff --git a/example-specs/task/nipype/afni/t_smooth.yaml b/example-specs/task/nipype/afni/t_smooth.yaml index 4a29400e..2f1b8822 100644 --- a/example-specs/task/nipype/afni/t_smooth.yaml +++ b/example-specs/task/nipype/afni/t_smooth.yaml @@ -152,7 +152,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dTSmooth adaptive: '5' # type=int|default=0: use adaptive mean filtering of width N (where N must be odd and bigger than 3). diff --git a/example-specs/task/nipype/afni/t_stat.yaml b/example-specs/task/nipype/afni/t_stat.yaml index 67dc3bfa..f00dfece 100644 --- a/example-specs/task/nipype/afni/t_stat.yaml +++ b/example-specs/task/nipype/afni/t_stat.yaml @@ -137,7 +137,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dTstat args: '"-mean"' # type=str|default='': Additional parameters to the command diff --git a/example-specs/task/nipype/afni/undump.yaml b/example-specs/task/nipype/afni/undump.yaml index 1e676425..0be1de71 100644 --- a/example-specs/task/nipype/afni/undump.yaml +++ b/example-specs/task/nipype/afni/undump.yaml @@ -164,7 +164,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: input file to 3dUndump, whose geometry will determinethe geometry of the output out_file: '"structural_undumped.nii"' # type=file: assembled file diff --git a/example-specs/task/nipype/afni/unifize.yaml b/example-specs/task/nipype/afni/unifize.yaml index 898ba78e..092b0876 100644 --- a/example-specs/task/nipype/afni/unifize.yaml +++ b/example-specs/task/nipype/afni/unifize.yaml @@ -180,7 +180,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: input file to 3dUnifize out_file: '"structural_unifized.nii"' # type=file: unifized file diff --git a/example-specs/task/nipype/afni/volreg.yaml b/example-specs/task/nipype/afni/volreg.yaml index bc003cc9..b7ff805d 100644 --- a/example-specs/task/nipype/afni/volreg.yaml +++ b/example-specs/task/nipype/afni/volreg.yaml @@ -227,7 +227,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dvolreg args: '"-Fourier -twopass"' # type=str|default='': Additional parameters to the command @@ -246,7 +246,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dvolreg interp: '"cubic"' # type=enum|default='Fourier'|allowed['Fourier','cubic','heptic','linear','quintic']: spatial interpolation methods [default = heptic] @@ -254,7 +254,7 @@ doctests: # type=bool|default=False: more detailed description of the process zpad: '1' # type=int|default=0: Zeropad around the edges by 'n' voxels during rotations - basefile: + basefile: '"functional.nii"' # type=file|default=: base file for registration out_file: '"rm.epi.volreg.r1"' # type=file: registered file diff --git a/example-specs/task/nipype/afni/warp.yaml b/example-specs/task/nipype/afni/warp.yaml index 6dd7d8e0..70332d87 100644 --- a/example-specs/task/nipype/afni/warp.yaml +++ b/example-specs/task/nipype/afni/warp.yaml @@ -196,7 +196,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: input file to 3dWarp deoblique: 'True' # type=bool|default=False: transform dataset from oblique to cardinal @@ -214,7 +214,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: input file to 3dWarp newgrid: '1.0' # type=float|default=0.0: specify grid of this size (mm) diff --git a/example-specs/task/nipype/afni/z_cut_up.yaml b/example-specs/task/nipype/afni/z_cut_up.yaml index d724a5e8..402baca7 100644 --- a/example-specs/task/nipype/afni/z_cut_up.yaml +++ b/example-specs/task/nipype/afni/z_cut_up.yaml @@ -133,7 +133,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file to 3dZcutup out_file: '"functional_zcutup.nii"' # type=file: output file diff --git a/example-specs/task/nipype/afni/zcat.yaml b/example-specs/task/nipype/afni/zcat.yaml index f2e17845..feabf411 100644 --- a/example-specs/task/nipype/afni/zcat.yaml +++ b/example-specs/task/nipype/afni/zcat.yaml @@ -137,7 +137,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["functional2.nii", "functional3.nii"]' # type=inputmultiobject|default=[]: out_file: '"cat_functional.nii"' # type=file: output file diff --git a/example-specs/task/nipype/afni/zeropad.yaml b/example-specs/task/nipype/afni/zeropad.yaml index fd943cd7..e8743b3f 100644 --- a/example-specs/task/nipype/afni/zeropad.yaml +++ b/example-specs/task/nipype/afni/zeropad.yaml @@ -172,7 +172,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '"functional.nii"' # type=file|default=: input dataset out_file: '"pad_functional.nii"' # type=file: output file diff --git a/example-specs/task/nipype/ants/affine_initializer.yaml b/example-specs/task/nipype/ants/affine_initializer.yaml index dac8edfc..1d7dc03e 100644 --- a/example-specs/task/nipype/ants/affine_initializer.yaml +++ b/example-specs/task/nipype/ants/affine_initializer.yaml @@ -134,9 +134,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - fixed_image: + fixed_image: '"fixed1.nii"' # type=file|default=: reference image - moving_image: + moving_image: '"moving1.nii"' # type=file|default=: moving image imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/ants/ants.yaml b/example-specs/task/nipype/ants/ants.yaml index 2d0f9219..94f2ed69 100644 --- a/example-specs/task/nipype/ants/ants.yaml +++ b/example-specs/task/nipype/ants/ants.yaml @@ -215,9 +215,9 @@ doctests: # type=str|default='out': metric: '["CC"]' # type=list|default=[]: - fixed_image: + fixed_image: '["T1.nii"]' # type=inputmultiobject|default=[]: image to which the moving image is warped - moving_image: + moving_image: '["resting.nii"]' # type=inputmultiobject|default=[]: image to apply transformation to (generally a coregisteredfunctional) metric_weight: '[1.0]' # type=list|default=[1.0]: the metric weight(s) for each stage. The weights must sum to 1 per stage. diff --git a/example-specs/task/nipype/ants/ants_introduction.yaml b/example-specs/task/nipype/ants/ants_introduction.yaml index 710529d2..04e3516d 100644 --- a/example-specs/task/nipype/ants/ants_introduction.yaml +++ b/example-specs/task/nipype/ants/ants_introduction.yaml @@ -148,9 +148,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - reference_image: + reference_image: '"Template_6.nii"' # type=file|default=: template file to warp to - input_image: + input_image: '"structural.nii"' # type=file|default=: input image to warp to template max_iterations: '[30,90,20]' # type=list|default=[]: maximum number of iterations (must be list of integers in the form [J,K,L...]: J = coarsest resolution iterations, K = middle resolution iterations, L = fine resolution iterations diff --git a/example-specs/task/nipype/ants/apply_transforms.yaml b/example-specs/task/nipype/ants/apply_transforms.yaml index eba0fbbb..58e0dba8 100644 --- a/example-specs/task/nipype/ants/apply_transforms.yaml +++ b/example-specs/task/nipype/ants/apply_transforms.yaml @@ -295,9 +295,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"moving1.nii"' # type=file|default=: image to apply transformation to (generally a coregistered functional) - reference_image: + reference_image: '"fixed1.nii"' # type=file|default=: reference image space that you wish to warp INTO transforms: '"identity"' # type=inputmultiobject|default=[]: transform files: will be applied in reverse order. For example, the last specified transform will be applied first. @@ -314,9 +314,9 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=2|allowed[2,3,4]: This option forces the image to be treated as a specified-dimensional image. If not specified, antsWarp tries to infer the dimensionality from the input image. - input_image: + input_image: '"moving1.nii"' # type=file|default=: image to apply transformation to (generally a coregistered functional) - reference_image: + reference_image: '"fixed1.nii"' # type=file|default=: reference image space that you wish to warp INTO output_image: '"deformed_moving1.nii"' # type=file: Warped image @@ -342,9 +342,9 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=2|allowed[2,3,4]: This option forces the image to be treated as a specified-dimensional image. If not specified, antsWarp tries to infer the dimensionality from the input image. - input_image: + input_image: '"moving1.nii"' # type=file|default=: image to apply transformation to (generally a coregistered functional) - reference_image: + reference_image: '"fixed1.nii"' # type=file|default=: reference image space that you wish to warp INTO output_image: '"deformed_moving1.nii"' # type=file: Warped image @@ -372,9 +372,9 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=2|allowed[2,3,4]: This option forces the image to be treated as a specified-dimensional image. If not specified, antsWarp tries to infer the dimensionality from the input image. - input_image: + input_image: '"moving1.nii"' # type=file|default=: image to apply transformation to (generally a coregistered functional) - reference_image: + reference_image: '"fixed1.nii"' # type=file|default=: reference image space that you wish to warp INTO output_image: '"deformed_moving1.nii"' # type=file: Warped image diff --git a/example-specs/task/nipype/ants/apply_transforms_to_points.yaml b/example-specs/task/nipype/ants/apply_transforms_to_points.yaml index 4fd4309d..1c2fc6a7 100644 --- a/example-specs/task/nipype/ants/apply_transforms_to_points.yaml +++ b/example-specs/task/nipype/ants/apply_transforms_to_points.yaml @@ -137,9 +137,9 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=2|allowed[2,3,4]: This option forces the image to be treated as a specified-dimensional image. If not specified, antsWarp tries to infer the dimensionality from the input image. - input_file: + input_file: '"moving.csv"' # type=file|default=: Currently, the only input supported is a csv file with columns including x,y (2D), x,y,z (3D) or x,y,z,t,label (4D) column headers. The points should be defined in physical space. If in doubt how to convert coordinates from your files to the space required by antsApplyTransformsToPoints try creating/drawing a simple label volume with only one voxel set to 1 and all others set to 0. Write down the voxel coordinates. Then use ImageMaths LabelStats to find out what coordinates for this voxel antsApplyTransformsToPoints is expecting. - transforms: + transforms: '["trans.mat", "ants_Warp.nii.gz"]' # type=list|default=[]: transforms that will be applied to the points invert_transform_flags: '[False, False]' # type=list|default=[]: list indicating if a transform should be reversed diff --git a/example-specs/task/nipype/ants/atropos.yaml b/example-specs/task/nipype/ants/atropos.yaml index 5d28ba86..386895a8 100644 --- a/example-specs/task/nipype/ants/atropos.yaml +++ b/example-specs/task/nipype/ants/atropos.yaml @@ -415,9 +415,9 @@ doctests: # type=enum|default='Random'|allowed['KMeans','Otsu','PriorLabelImage','PriorProbabilityImages','Random']: dimension: '3' # type=enum|default=3|allowed[2,3,4]: image dimension (2, 3, or 4) - intensity_images: + intensity_images: '"structural.nii"' # type=inputmultiobject|default=[]: - mask_image: + mask_image: '"mask.nii"' # type=file|default=: number_of_tissue_classes: '2' # type=int|default=0: @@ -458,9 +458,9 @@ doctests: # type=list|default=[]: dimension: '3' # type=enum|default=3|allowed[2,3,4]: image dimension (2, 3, or 4) - intensity_images: + intensity_images: '"structural.nii"' # type=inputmultiobject|default=[]: - mask_image: + mask_image: '"mask.nii"' # type=file|default=: number_of_tissue_classes: '2' # type=int|default=0: @@ -505,9 +505,9 @@ doctests: # type=float|default=0.0: dimension: '3' # type=enum|default=3|allowed[2,3,4]: image dimension (2, 3, or 4) - intensity_images: + intensity_images: '"structural.nii"' # type=inputmultiobject|default=[]: - mask_image: + mask_image: '"mask.nii"' # type=file|default=: number_of_tissue_classes: '2' # type=int|default=0: @@ -552,9 +552,9 @@ doctests: # type=float|default=0.0: dimension: '3' # type=enum|default=3|allowed[2,3,4]: image dimension (2, 3, or 4) - intensity_images: + intensity_images: '"structural.nii"' # type=inputmultiobject|default=[]: - mask_image: + mask_image: '"mask.nii"' # type=file|default=: likelihood_model: '"Gaussian"' # type=str|default='': diff --git a/example-specs/task/nipype/ants/average_affine_transform.yaml b/example-specs/task/nipype/ants/average_affine_transform.yaml index eb2d770a..e4ea3876 100644 --- a/example-specs/task/nipype/ants/average_affine_transform.yaml +++ b/example-specs/task/nipype/ants/average_affine_transform.yaml @@ -124,7 +124,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=3|allowed[2,3]: image dimension (2 or 3) - transforms: + transforms: '["trans.mat", "func_to_struct.mat"]' # type=inputmultiobject|default=[]: transforms to average output_affine_transform: '"MYtemplatewarp.mat"' # type=file|default=: Outputfname.txt: the name of the resulting transform. diff --git a/example-specs/task/nipype/ants/average_images.yaml b/example-specs/task/nipype/ants/average_images.yaml index 15817cba..10296843 100644 --- a/example-specs/task/nipype/ants/average_images.yaml +++ b/example-specs/task/nipype/ants/average_images.yaml @@ -137,7 +137,7 @@ doctests: # type=file|default='average.nii': the name of the resulting image. normalize: 'True' # type=bool|default=False: Normalize: if true, the 2nd image is divided by its mean. This will select the largest image to average into. - images: + images: '["rc1s1.nii", "rc1s1.nii"]' # type=inputmultiobject|default=[]: image to apply transformation to (generally a coregistered functional) imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/ants/brain_extraction.yaml b/example-specs/task/nipype/ants/brain_extraction.yaml index df8a8400..7edbfaa6 100644 --- a/example-specs/task/nipype/ants/brain_extraction.yaml +++ b/example-specs/task/nipype/ants/brain_extraction.yaml @@ -184,11 +184,11 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=3|allowed[2,3]: image dimension (2 or 3) - anatomical_image: + anatomical_image: '"T1.nii.gz"' # type=file|default=: Structural image, typically T1. If more than one anatomical image is specified, subsequently specified images are used during the segmentation process. However, only the first image is used in the registration of priors. Our suggestion would be to specify the T1 as the first image. Anatomical template created using e.g. LPBA40 data set with buildtemplateparallel.sh in ANTs. - brain_template: + brain_template: '"study_template.nii.gz"' # type=file|default=: Anatomical template created using e.g. LPBA40 data set with buildtemplateparallel.sh in ANTs. - brain_probability_mask: + brain_probability_mask: '"ProbabilityMaskOfStudyTemplate.nii.gz"' # type=file|default=: Brain probability mask created using e.g. LPBA40 data set which have brain masks defined, and warped to anatomical template and averaged resulting in a probability image. imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/ants/buildtemplateparallel.yaml b/example-specs/task/nipype/ants/buildtemplateparallel.yaml index a712377c..95b1749b 100644 --- a/example-specs/task/nipype/ants/buildtemplateparallel.yaml +++ b/example-specs/task/nipype/ants/buildtemplateparallel.yaml @@ -147,7 +147,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["T1.nii", "structural.nii"]' # type=list|default=[]: list of images to generate template from max_iterations: '[30, 90, 20]' # type=list|default=[]: maximum number of iterations (must be list of integers in the form [J,K,L...]: J = coarsest resolution iterations, K = middle resolution iterations, L = fine resolution iterations diff --git a/example-specs/task/nipype/ants/compose_multi_transform.yaml b/example-specs/task/nipype/ants/compose_multi_transform.yaml index fe0dce81..eedf479e 100644 --- a/example-specs/task/nipype/ants/compose_multi_transform.yaml +++ b/example-specs/task/nipype/ants/compose_multi_transform.yaml @@ -131,7 +131,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=3|allowed[2,3]: image dimension (2 or 3) - transforms: + transforms: '["struct_to_template.mat", "func_to_struct.mat"]' # type=inputmultiobject|default=[]: transforms to average imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/ants/composite_transform_util.yaml b/example-specs/task/nipype/ants/composite_transform_util.yaml index 70147e30..9a108932 100644 --- a/example-specs/task/nipype/ants/composite_transform_util.yaml +++ b/example-specs/task/nipype/ants/composite_transform_util.yaml @@ -170,7 +170,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. process: '"disassemble"' # type=enum|default='assemble'|allowed['assemble','disassemble']: What to do with the transform inputs (assemble or disassemble) - in_file: + in_file: '"output_Composite.h5"' # type=inputmultiobject|default=[]: Input transform file(s) imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item @@ -188,7 +188,7 @@ doctests: out_file: '"my.h5"' # type=file: Compound transformation file # type=file|default=: Output file path (only used for disassembly). - in_file: + in_file: '["AffineTransform.mat", "DisplacementFieldTransform.nii.gz"]' # type=inputmultiobject|default=[]: Input transform file(s) imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/ants/convert_scalar_image_to_rgb.yaml b/example-specs/task/nipype/ants/convert_scalar_image_to_rgb.yaml index fb24feea..8bfd51d0 100644 --- a/example-specs/task/nipype/ants/convert_scalar_image_to_rgb.yaml +++ b/example-specs/task/nipype/ants/convert_scalar_image_to_rgb.yaml @@ -146,7 +146,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=3|allowed[2,3]: image dimension (2 or 3) - input_image: + input_image: '"T1.nii.gz"' # type=file|default=: Main input is a 3-D grayscale image. colormap: '"jet"' # type=enum|default='grey'|allowed['autumn','blue','cool','copper','custom','green','grey','hot','hsv','jet','overunder','red','spring','summer','winter']: Select a colormap diff --git a/example-specs/task/nipype/ants/cortical_thickness.yaml b/example-specs/task/nipype/ants/cortical_thickness.yaml index d12f14de..498b7dea 100644 --- a/example-specs/task/nipype/ants/cortical_thickness.yaml +++ b/example-specs/task/nipype/ants/cortical_thickness.yaml @@ -208,15 +208,15 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=3|allowed[2,3]: image dimension (2 or 3) - anatomical_image: + anatomical_image: '"T1.nii.gz"' # type=file|default=: Structural *intensity* image, typically T1. If more than one anatomical image is specified, subsequently specified images are used during the segmentation process. However, only the first image is used in the registration of priors. Our suggestion would be to specify the T1 as the first image. - brain_template: + brain_template: '"study_template.nii.gz"' # type=file|default=: Anatomical *intensity* template (possibly created using a population data set with buildtemplateparallel.sh in ANTs). This template is *not* skull-stripped. - brain_probability_mask: + brain_probability_mask: '"ProbabilityMaskOfStudyTemplate.nii.gz"' # type=file|default=: brain probability mask in template space - segmentation_priors: + segmentation_priors: '["BrainSegmentationPrior01.nii.gz","BrainSegmentationPrior02.nii.gz","BrainSegmentationPrior03.nii.gz","BrainSegmentationPrior04.nii.gz"]' # type=inputmultiobject|default=[]: - t1_registration_template: + t1_registration_template: '"brain_study_template.nii.gz"' # type=file|default=: Anatomical *intensity* template (assumed to be skull-stripped). A common case would be where this would be the same template as specified in the -e option which is not skull stripped. imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/ants/create_jacobian_determinant_image.yaml b/example-specs/task/nipype/ants/create_jacobian_determinant_image.yaml index d524d09a..9376585c 100644 --- a/example-specs/task/nipype/ants/create_jacobian_determinant_image.yaml +++ b/example-specs/task/nipype/ants/create_jacobian_determinant_image.yaml @@ -127,9 +127,9 @@ doctests: # '.mock()' method of the corresponding class is used instead. imageDimension: '3' # type=enum|default=3|allowed[2,3]: image dimension (2 or 3) - deformationField: + deformationField: '"ants_Warp.nii.gz"' # type=file|default=: deformation transformation file - outputImage: + outputImage: '"out_name.nii.gz"' # type=file|default=: output filename imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/ants/create_tiled_mosaic.yaml b/example-specs/task/nipype/ants/create_tiled_mosaic.yaml index 3d370ee9..bd77eb72 100644 --- a/example-specs/task/nipype/ants/create_tiled_mosaic.yaml +++ b/example-specs/task/nipype/ants/create_tiled_mosaic.yaml @@ -162,11 +162,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"T1.nii.gz"' # type=file|default=: Main input is a 3-D grayscale image. - rgb_image: + rgb_image: '"rgb.nii.gz"' # type=file|default=: An optional Rgb image can be added as an overlay.It must have the same imagegeometry as the input grayscale image. - mask_image: + mask_image: '"mask.nii.gz"' # type=file|default=: Specifies the ROI of the RGB voxels used. output_image: '"output.png"' # type=file: image file diff --git a/example-specs/task/nipype/ants/denoise_image.yaml b/example-specs/task/nipype/ants/denoise_image.yaml index a0e0ea7c..b2e8b304 100644 --- a/example-specs/task/nipype/ants/denoise_image.yaml +++ b/example-specs/task/nipype/ants/denoise_image.yaml @@ -203,7 +203,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=2|allowed[2,3,4]: This option forces the image to be treated as a specified-dimensional image. If not specified, the program tries to infer the dimensionality from the input image. - input_image: + input_image: '"im1.nii"' # type=file|default=: A scalar image is expected as input for noise correction. imports: *id001 # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item @@ -234,7 +234,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"im1.nii"' # type=file|default=: A scalar image is expected as input for noise correction. save_noise: 'True' # type=bool|default=False: True if the estimated noise should be saved to file. diff --git a/example-specs/task/nipype/ants/image_math.yaml b/example-specs/task/nipype/ants/image_math.yaml index c453d829..32a6b6b3 100644 --- a/example-specs/task/nipype/ants/image_math.yaml +++ b/example-specs/task/nipype/ants/image_math.yaml @@ -246,7 +246,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - op1: + op1: '"structural.nii"' # type=file|default=: first operator operation: '"+"' # type=enum|default='m'|allowed['+','-','/','4DTensorTo3DTensor','Byte','Canny','Convolve','CorruptImage','D','Decision','ExtractContours','ExtractSlice','ExtractVectorComponent','FillHoles','Finite','FlattenImage','G','GC','GD','GE','GO','GetLargestComponent','Grad','LabelStats','Laplacian','Lipschitz','MC','MD','ME','MO','MTR','MaurerDistance','Neg','NeighborhoodStats','Normalize','PValueImage','PadImage','Project','ReplaceVoxelValue','ReplicateDisplacement','ReplicateImage','RescaleImage','SetTimeSpacing','SetTimeSpacingWarp','Sharpen','SigmoidImage','TensorAxialDiffusion','TensorColor','TensorEigenvalue','TensorFA','TensorFADenominator','TensorFANumerator','TensorMask','TensorMeanDiffusion','TensorRadialDiffusion','TensorToVector','TensorToVectorComponent','ThresholdAtMean','Translate','TriPlanarView','TruncateImageIntensity','UnsharpMask','WindowImage','^','abs','addtozero','exp','m','max','mean','overadd','stack','total','v+','v-','vm','vtotal']: mathematical operations @@ -263,7 +263,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - op1: + op1: '"structural.nii"' # type=file|default=: first operator operation: '"Project"' # type=enum|default='m'|allowed['+','-','/','4DTensorTo3DTensor','Byte','Canny','Convolve','CorruptImage','D','Decision','ExtractContours','ExtractSlice','ExtractVectorComponent','FillHoles','Finite','FlattenImage','G','GC','GD','GE','GO','GetLargestComponent','Grad','LabelStats','Laplacian','Lipschitz','MC','MD','ME','MO','MTR','MaurerDistance','Neg','NeighborhoodStats','Normalize','PValueImage','PadImage','Project','ReplaceVoxelValue','ReplicateDisplacement','ReplicateImage','RescaleImage','SetTimeSpacing','SetTimeSpacingWarp','Sharpen','SigmoidImage','TensorAxialDiffusion','TensorColor','TensorEigenvalue','TensorFA','TensorFADenominator','TensorFANumerator','TensorMask','TensorMeanDiffusion','TensorRadialDiffusion','TensorToVector','TensorToVectorComponent','ThresholdAtMean','Translate','TriPlanarView','TruncateImageIntensity','UnsharpMask','WindowImage','^','abs','addtozero','exp','m','max','mean','overadd','stack','total','v+','v-','vm','vtotal']: mathematical operations @@ -280,7 +280,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - op1: + op1: '"structural.nii"' # type=file|default=: first operator operation: '"G"' # type=enum|default='m'|allowed['+','-','/','4DTensorTo3DTensor','Byte','Canny','Convolve','CorruptImage','D','Decision','ExtractContours','ExtractSlice','ExtractVectorComponent','FillHoles','Finite','FlattenImage','G','GC','GD','GE','GO','GetLargestComponent','Grad','LabelStats','Laplacian','Lipschitz','MC','MD','ME','MO','MTR','MaurerDistance','Neg','NeighborhoodStats','Normalize','PValueImage','PadImage','Project','ReplaceVoxelValue','ReplicateDisplacement','ReplicateImage','RescaleImage','SetTimeSpacing','SetTimeSpacingWarp','Sharpen','SigmoidImage','TensorAxialDiffusion','TensorColor','TensorEigenvalue','TensorFA','TensorFADenominator','TensorFANumerator','TensorMask','TensorMeanDiffusion','TensorRadialDiffusion','TensorToVector','TensorToVectorComponent','ThresholdAtMean','Translate','TriPlanarView','TruncateImageIntensity','UnsharpMask','WindowImage','^','abs','addtozero','exp','m','max','mean','overadd','stack','total','v+','v-','vm','vtotal']: mathematical operations @@ -297,7 +297,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - op1: + op1: '"structural.nii"' # type=file|default=: first operator operation: '"TruncateImageIntensity"' # type=enum|default='m'|allowed['+','-','/','4DTensorTo3DTensor','Byte','Canny','Convolve','CorruptImage','D','Decision','ExtractContours','ExtractSlice','ExtractVectorComponent','FillHoles','Finite','FlattenImage','G','GC','GD','GE','GO','GetLargestComponent','Grad','LabelStats','Laplacian','Lipschitz','MC','MD','ME','MO','MTR','MaurerDistance','Neg','NeighborhoodStats','Normalize','PValueImage','PadImage','Project','ReplaceVoxelValue','ReplicateDisplacement','ReplicateImage','RescaleImage','SetTimeSpacing','SetTimeSpacingWarp','Sharpen','SigmoidImage','TensorAxialDiffusion','TensorColor','TensorEigenvalue','TensorFA','TensorFADenominator','TensorFANumerator','TensorMask','TensorMeanDiffusion','TensorRadialDiffusion','TensorToVector','TensorToVectorComponent','ThresholdAtMean','Translate','TriPlanarView','TruncateImageIntensity','UnsharpMask','WindowImage','^','abs','addtozero','exp','m','max','mean','overadd','stack','total','v+','v-','vm','vtotal']: mathematical operations diff --git a/example-specs/task/nipype/ants/joint_fusion.yaml b/example-specs/task/nipype/ants/joint_fusion.yaml index 7039070a..8eb6122a 100644 --- a/example-specs/task/nipype/ants/joint_fusion.yaml +++ b/example-specs/task/nipype/ants/joint_fusion.yaml @@ -362,7 +362,7 @@ doctests: # type=file|default=: The output label fusion image. atlas_image: '[ ["rc1s1.nii","rc1s2.nii"] ]' # type=list|default=[]: The atlas image (or multimodal atlas images) assumed to be aligned to a common image domain. - atlas_segmentation_image: + atlas_segmentation_image: '["segmentation0.nii.gz"]' # type=inputmultiobject|default=[]: The atlas segmentation images. For performing label fusion the number of specified segmentations should be identical to the number of atlas image sets. target_image: '["im1.nii"]' # type=list|default=[]: The target image (or multimodal target images) assumed to be aligned to a common image domain. @@ -392,7 +392,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. atlas_image: '[ ["rc1s1.nii","rc1s2.nii"],["rc2s1.nii","rc2s2.nii"] ]' # type=list|default=[]: The atlas image (or multimodal atlas images) assumed to be aligned to a common image domain. - atlas_segmentation_image: + atlas_segmentation_image: '["segmentation0.nii.gz","segmentation1.nii.gz"]' # type=inputmultiobject|default=[]: The atlas segmentation images. For performing label fusion the number of specified segmentations should be identical to the number of atlas image sets. imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item @@ -430,7 +430,7 @@ doctests: # type=list|default=[3, 3, 3]: Search radius for similarity measures. Default = 3x3x3. One can also specify an image where the value at the voxel specifies the isotropic search radius at that voxel. verbose: 'True' # type=bool|default=False: Verbose output. - exclusion_image: + exclusion_image: '["roi01.nii", "roi02.nii"]' # type=list|default=[]: Specify an exclusion region for the given label. exclusion_image_label: '["1","2"]' # type=list|default=[]: Specify a label for the exclusion region. diff --git a/example-specs/task/nipype/ants/kelly_kapowski.yaml b/example-specs/task/nipype/ants/kelly_kapowski.yaml index b8b533d6..18274e71 100644 --- a/example-specs/task/nipype/ants/kelly_kapowski.yaml +++ b/example-specs/task/nipype/ants/kelly_kapowski.yaml @@ -182,7 +182,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=3|allowed[2,3]: image dimension (2 or 3) - segmentation_image: + segmentation_image: '"segmentation0.nii.gz"' # type=file|default=: A segmentation image must be supplied labeling the gray and white matters. Default values = 2 and 3, respectively. convergence: '"[45,0.0,10]"' # type=str|default='[50,0.001,10]': Convergence is determined by fitting a line to the normalized energy profile of the last N iterations (where N is specified by the window size) and determining the slope which is then compared with the convergence threshold. diff --git a/example-specs/task/nipype/ants/label_geometry.yaml b/example-specs/task/nipype/ants/label_geometry.yaml index 21fc257c..74e485a3 100644 --- a/example-specs/task/nipype/ants/label_geometry.yaml +++ b/example-specs/task/nipype/ants/label_geometry.yaml @@ -151,7 +151,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=3|allowed[2,3]: image dimension (2 or 3) - label_image: + label_image: '"atlas.nii.gz"' # type=file|default=: label image to use for extracting geometry measures imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item @@ -164,7 +164,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - intensity_image: + intensity_image: '"ants_Warp.nii.gz"' # type=file|default='[]': Intensity image to extract values from. This is an optional input imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/ants/laplacian_thickness.yaml b/example-specs/task/nipype/ants/laplacian_thickness.yaml index 23d4a392..68853a30 100644 --- a/example-specs/task/nipype/ants/laplacian_thickness.yaml +++ b/example-specs/task/nipype/ants/laplacian_thickness.yaml @@ -158,9 +158,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_wm: + input_wm: '"white_matter.nii.gz"' # type=file|default=: white matter segmentation image - input_gm: + input_gm: '"gray_matter.nii.gz"' # type=file|default=: gray matter segmentation image imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/ants/measure_image_similarity.yaml b/example-specs/task/nipype/ants/measure_image_similarity.yaml index cc086bec..a146fd7e 100644 --- a/example-specs/task/nipype/ants/measure_image_similarity.yaml +++ b/example-specs/task/nipype/ants/measure_image_similarity.yaml @@ -167,9 +167,9 @@ doctests: # type=enum|default=2|allowed[2,3,4]: Dimensionality of the fixed/moving image pair metric: '"MI"' # type=enum|default='CC'|allowed['CC','Demons','GC','MI','Mattes','MeanSquares']: - fixed_image: + fixed_image: '"T1.nii"' # type=file|default=: Image to which the moving image is warped - moving_image: + moving_image: '"resting.nii"' # type=file|default=: Image to apply transformation to (generally a coregistered functional) metric_weight: '1.0' # type=float|default=1.0: The "metricWeight" variable is not used. @@ -179,9 +179,9 @@ doctests: # type=enum|default='None'|allowed['None','Random','Regular']: Manner of choosing point set over which to optimize the metric. Defaults to "None" (i.e. a dense sampling of one sample per voxel). sampling_percentage: '1.0' # type=range|default=None: Percentage of points accessible to the sampling strategy over which to optimize the metric. - fixed_image_mask: + fixed_image_mask: '"mask.nii"' # type=file|default=: mask used to limit metric sampling region of the fixed image - moving_image_mask: + moving_image_mask: '"mask.nii.gz"' # type=file|default=: mask used to limit metric sampling region of the moving image imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/ants/multiply_images.yaml b/example-specs/task/nipype/ants/multiply_images.yaml index aacb7cdb..76dcb835 100644 --- a/example-specs/task/nipype/ants/multiply_images.yaml +++ b/example-specs/task/nipype/ants/multiply_images.yaml @@ -132,7 +132,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=3|allowed[2,3]: image dimension (2 or 3) - first_input: + first_input: '"moving2.nii"' # type=file|default=: image 1 second_input: '0.25' # type=traitcompound|default=None: image 2 or multiplication weight diff --git a/example-specs/task/nipype/ants/n4_bias_field_correction.yaml b/example-specs/task/nipype/ants/n4_bias_field_correction.yaml index bb3f0d73..a1e5dd7c 100644 --- a/example-specs/task/nipype/ants/n4_bias_field_correction.yaml +++ b/example-specs/task/nipype/ants/n4_bias_field_correction.yaml @@ -306,7 +306,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. dimension: '3' # type=enum|default=3|allowed[2,3,4]: image dimension (2, 3 or 4) - input_image: + input_image: '"structural.nii"' # type=file|default=: input for bias correction. Negative values or values close to zero should be processed prior to correction bspline_fitting_distance: '300' # type=float|default=0.0: @@ -351,7 +351,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"structural.nii"' # type=file|default=: input for bias correction. Negative values or values close to zero should be processed prior to correction save_bias: 'True' # type=bool|default=False: True if the estimated bias should be saved to file. @@ -368,7 +368,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"structural.nii"' # type=file|default=: input for bias correction. Negative values or values close to zero should be processed prior to correction dimension: '3' # type=enum|default=3|allowed[2,3,4]: image dimension (2, 3 or 4) diff --git a/example-specs/task/nipype/ants/registration.yaml b/example-specs/task/nipype/ants/registration.yaml index d066ce5c..e858cf17 100644 --- a/example-specs/task/nipype/ants/registration.yaml +++ b/example-specs/task/nipype/ants/registration.yaml @@ -848,13 +848,13 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - fixed_image: + fixed_image: '"fixed1.nii"' # type=inputmultiobject|default=[]: Image to which the moving_image should be transformed(usually a structural image) - moving_image: + moving_image: '"moving1.nii"' # type=inputmultiobject|default=[]: Image that will be registered to the space of fixed_image. This is theimage on which the transformations will be applied to output_transform_prefix: '"output_"' # type=str|default='transform': - initial_moving_transform: + initial_moving_transform: '"trans.mat"' # type=inputmultiobject|default=[]: A transform or a list of transforms that should be applied before the registration begins. Note that, when a list is given, the transformations are applied in reverse order. transforms: '["Affine", "SyN"]' # type=list|default=[]: @@ -979,7 +979,7 @@ doctests: save_state: '"trans.mat"' # type=file: The saved registration state to be restored # type=file|default=: Filename for saving the internal restorable state of the registration - restore_state: + restore_state: '"trans.mat"' # type=file|default=: Filename for restoring the internal restorable state of the registration initialize_transforms_per_stage: 'True' # type=bool|default=False: Initialize linear transforms from the previous stage. By enabling this option, the current linear stage transform is directly initialized from the previous stages linear transform; this allows multiple linear stages to be run where each stage directly updates the estimated linear transform from the previous stage. (e.g. Translation -> Rigid -> Affine). @@ -1009,9 +1009,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - fixed_image: + fixed_image: '"fixed1.nii"' # type=inputmultiobject|default=[]: Image to which the moving_image should be transformed(usually a structural image) - moving_image: + moving_image: '"moving1.nii"' # type=inputmultiobject|default=[]: Image that will be registered to the space of fixed_image. This is theimage on which the transformations will be applied to metric: '["Mattes", ["Mattes", "CC"]]' # type=list|default=[]: the metric(s) to use for each stage. Note that multiple metrics per stage are not supported in ANTS 1.9.1 and earlier. @@ -1034,9 +1034,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - fixed_image: + fixed_image: '["fixed1.nii", "fixed2.nii"]' # type=inputmultiobject|default=[]: Image to which the moving_image should be transformed(usually a structural image) - moving_image: + moving_image: '["moving1.nii", "moving2.nii"]' # type=inputmultiobject|default=[]: Image that will be registered to the space of fixed_image. This is theimage on which the transformations will be applied to imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item @@ -1107,7 +1107,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - initial_moving_transform: + initial_moving_transform: '["func_to_struct.mat", "ants_Warp.nii.gz"]' # type=inputmultiobject|default=[]: A transform or a list of transforms that should be applied before the registration begins. Note that, when a list is given, the transformations are applied in reverse order. invert_initial_moving_transform: '[False, False]' # type=inputmultiobject|default=[]: One boolean or a list of booleans that indicatewhether the inverse(s) of the transform(s) definedin initial_moving_transform should be used. diff --git a/example-specs/task/nipype/ants/registration_syn_quick.yaml b/example-specs/task/nipype/ants/registration_syn_quick.yaml index 70a63846..5ba7dfd3 100644 --- a/example-specs/task/nipype/ants/registration_syn_quick.yaml +++ b/example-specs/task/nipype/ants/registration_syn_quick.yaml @@ -184,9 +184,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - fixed_image: + fixed_image: '"fixed1.nii"' # type=inputmultiobject|default=[]: Fixed image or source image or reference image - moving_image: + moving_image: '"moving1.nii"' # type=inputmultiobject|default=[]: Moving image or target image num_threads: '2' # type=int|default=1: Number of threads (default = 1) @@ -201,9 +201,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - fixed_image: + fixed_image: '["fixed1.nii", "fixed2.nii"]' # type=inputmultiobject|default=[]: Fixed image or source image or reference image - moving_image: + moving_image: '["moving1.nii", "moving2.nii"]' # type=inputmultiobject|default=[]: Moving image or target image num_threads: '2' # type=int|default=1: Number of threads (default = 1) diff --git a/example-specs/task/nipype/ants/resample_image_by_spacing.yaml b/example-specs/task/nipype/ants/resample_image_by_spacing.yaml index 7c61c1e9..88212944 100644 --- a/example-specs/task/nipype/ants/resample_image_by_spacing.yaml +++ b/example-specs/task/nipype/ants/resample_image_by_spacing.yaml @@ -217,7 +217,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"structural.nii"' # type=file|default=: input image file output_image: '"output.nii.gz"' # type=file: resampled file @@ -237,7 +237,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"structural.nii"' # type=file|default=: input image file output_image: '"output.nii.gz"' # type=file: resampled file @@ -259,7 +259,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"structural.nii"' # type=file|default=: input image file output_image: '"output.nii.gz"' # type=file: resampled file diff --git a/example-specs/task/nipype/ants/threshold_image.yaml b/example-specs/task/nipype/ants/threshold_image.yaml index beace54c..4e0b85c9 100644 --- a/example-specs/task/nipype/ants/threshold_image.yaml +++ b/example-specs/task/nipype/ants/threshold_image.yaml @@ -193,7 +193,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"structural.nii"' # type=file|default=: input image file output_image: '"output.nii.gz"' # type=file: resampled file @@ -219,7 +219,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"structural.nii"' # type=file|default=: input image file output_image: '"output.nii.gz"' # type=file: resampled file diff --git a/example-specs/task/nipype/ants/warp_image_multi_transform.yaml b/example-specs/task/nipype/ants/warp_image_multi_transform.yaml index ea6fde25..3e42e171 100644 --- a/example-specs/task/nipype/ants/warp_image_multi_transform.yaml +++ b/example-specs/task/nipype/ants/warp_image_multi_transform.yaml @@ -186,11 +186,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"structural.nii"' # type=file|default=: image to apply transformation to (generally a coregistered functional) - reference_image: + reference_image: '"ants_deformed.nii.gz"' # type=file|default=: reference image space that you wish to warp INTO - transformation_series: + transformation_series: '["ants_Warp.nii.gz","ants_Affine.txt"]' # type=inputmultiobject|default=[]: transformation file(s) to be applied imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item @@ -203,11 +203,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"diffusion_weighted.nii"' # type=file|default=: image to apply transformation to (generally a coregistered functional) - reference_image: + reference_image: '"functional.nii"' # type=file|default=: reference image space that you wish to warp INTO - transformation_series: + transformation_series: '["func2anat_coreg_Affine.txt","func2anat_InverseWarp.nii.gz", "dwi2anat_Warp.nii.gz","dwi2anat_coreg_Affine.txt"]' # type=inputmultiobject|default=[]: transformation file(s) to be applied invert_affine: '[1] # this will invert the 1st Affine file: "func2anat_coreg_Affine.txt"' # type=list|default=[]: List of Affine transformations to invert.E.g.: [1,4,5] inverts the 1st, 4th, and 5th Affines found in transformation_series. Note that indexing starts with 1 and does not include warp fields. Affine transformations are distinguished from warp fields by the word "affine" included in their filenames. diff --git a/example-specs/task/nipype/ants/warp_time_series_image_multi_transform.yaml b/example-specs/task/nipype/ants/warp_time_series_image_multi_transform.yaml index 3884b36d..5ec4697c 100644 --- a/example-specs/task/nipype/ants/warp_time_series_image_multi_transform.yaml +++ b/example-specs/task/nipype/ants/warp_time_series_image_multi_transform.yaml @@ -173,11 +173,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"resting.nii"' # type=file|default=: image to apply transformation to (generally a coregistered functional) - reference_image: + reference_image: '"ants_deformed.nii.gz"' # type=file|default=: reference image space that you wish to warp INTO - transformation_series: + transformation_series: '["ants_Warp.nii.gz","ants_Affine.txt"]' # type=inputmultiobject|default=[]: transformation file(s) to be applied imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item @@ -190,11 +190,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - input_image: + input_image: '"resting.nii"' # type=file|default=: image to apply transformation to (generally a coregistered functional) - reference_image: + reference_image: '"ants_deformed.nii.gz"' # type=file|default=: reference image space that you wish to warp INTO - transformation_series: + transformation_series: '["ants_Warp.nii.gz","ants_Affine.txt"]' # type=inputmultiobject|default=[]: transformation file(s) to be applied invert_affine: '[1] # # this will invert the 1st Affine file: ants_Affine.txt' # type=list|default=[]: List of Affine transformations to invert.E.g.: [1,4,5] inverts the 1st, 4th, and 5th Affines found in transformation_series. Note that indexing starts with 1 and does not include warp fields. Affine transformations are distinguished from warp fields by the word "affine" included in their filenames. diff --git a/example-specs/task/nipype/freesurfer/add_x_form_to_header.yaml b/example-specs/task/nipype/freesurfer/add_x_form_to_header.yaml index 207f942d..1fcb2fad 100644 --- a/example-specs/task/nipype/freesurfer/add_x_form_to_header.yaml +++ b/example-specs/task/nipype/freesurfer/add_x_form_to_header.yaml @@ -166,9 +166,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"norm.mgz"' # type=file|default=: input volume - transform: + transform: '"trans.mat"' # type=file|default=: xfm file imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/aparc_2_aseg.yaml b/example-specs/task/nipype/freesurfer/aparc_2_aseg.yaml index 985782bb..2a51e675 100644 --- a/example-specs/task/nipype/freesurfer/aparc_2_aseg.yaml +++ b/example-specs/task/nipype/freesurfer/aparc_2_aseg.yaml @@ -226,23 +226,23 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - lh_white: + lh_white: '"lh.pial"' # type=file|default=: Input file must be /surf/lh.white - rh_white: + rh_white: '"lh.pial"' # type=file|default=: Input file must be /surf/rh.white - lh_pial: + lh_pial: '"lh.pial"' # type=file|default=: Input file must be /surf/lh.pial - rh_pial: + rh_pial: '"lh.pial"' # type=file|default=: Input file must be /surf/rh.pial - lh_ribbon: + lh_ribbon: '"label.mgz"' # type=file|default=: Input file must be /mri/lh.ribbon.mgz - rh_ribbon: + rh_ribbon: '"label.mgz"' # type=file|default=: Input file must be /mri/rh.ribbon.mgz - ribbon: + ribbon: '"label.mgz"' # type=file|default=: Input file must be /mri/ribbon.mgz - lh_annotation: + lh_annotation: '"lh.pial"' # type=file|default=: Input file must be /label/lh.aparc.annot - rh_annotation: + rh_annotation: '"lh.pial"' # type=file|default=: Input file must be /label/rh.aparc.annot out_file: '"aparc+aseg.mgz"' # type=file: Output aseg file diff --git a/example-specs/task/nipype/freesurfer/apas_2_aseg.yaml b/example-specs/task/nipype/freesurfer/apas_2_aseg.yaml index 1f7ce546..31df5e7f 100644 --- a/example-specs/task/nipype/freesurfer/apas_2_aseg.yaml +++ b/example-specs/task/nipype/freesurfer/apas_2_aseg.yaml @@ -128,7 +128,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"aseg.mgz"' # type=file|default=: Input aparc+aseg.mgz out_file: '"output.mgz"' # type=file: Output aseg file diff --git a/example-specs/task/nipype/freesurfer/apply_vol_transform.yaml b/example-specs/task/nipype/freesurfer/apply_vol_transform.yaml index 5311dc29..bdbb9706 100644 --- a/example-specs/task/nipype/freesurfer/apply_vol_transform.yaml +++ b/example-specs/task/nipype/freesurfer/apply_vol_transform.yaml @@ -184,9 +184,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - source_file: + source_file: '"structural.nii"' # type=file|default=: Input volume you wish to transform - reg_file: + reg_file: '"register.dat"' # type=file|default=: tkRAS-to-tkRAS matrix (tkregister2 format) transformed_file: '"struct_warped.nii"' # type=file: Path to output file if used normally diff --git a/example-specs/task/nipype/freesurfer/bb_register.yaml b/example-specs/task/nipype/freesurfer/bb_register.yaml index 3da85166..99e8f145 100644 --- a/example-specs/task/nipype/freesurfer/bb_register.yaml +++ b/example-specs/task/nipype/freesurfer/bb_register.yaml @@ -187,7 +187,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. subject_id: '"me"' # type=str|default='': freesurfer subject id - source_file: + source_file: '"structural.nii"' # type=file|default=: source file to be registered init: '"header"' # type=enum|default='coreg'|allowed['best','coreg','fsl','header','rr','spm']: initialize registration with mri_coreg, spm, fsl, or header diff --git a/example-specs/task/nipype/freesurfer/binarize.yaml b/example-specs/task/nipype/freesurfer/binarize.yaml index 8f385c0d..bf25ed9f 100644 --- a/example-specs/task/nipype/freesurfer/binarize.yaml +++ b/example-specs/task/nipype/freesurfer/binarize.yaml @@ -182,7 +182,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: input volume min: '10' # type=float|default=0.0: min thresh diff --git a/example-specs/task/nipype/freesurfer/ca_label.yaml b/example-specs/task/nipype/freesurfer/ca_label.yaml index eec07a8c..321806f2 100644 --- a/example-specs/task/nipype/freesurfer/ca_label.yaml +++ b/example-specs/task/nipype/freesurfer/ca_label.yaml @@ -169,14 +169,14 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"norm.mgz"' # type=file|default=: Input volume for CALabel out_file: '"out.mgz"' # type=file: Output volume from CALabel # type=file|default=: Output file for CALabel - transform: + transform: '"trans.mat"' # type=file|default=: Input transform for CALabel - template: + template: '"Template_6.nii" # in practice use .gcs extension' # type=file|default=: Input template for CALabel imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/ca_normalize.yaml b/example-specs/task/nipype/freesurfer/ca_normalize.yaml index eaabedaf..b2152c20 100644 --- a/example-specs/task/nipype/freesurfer/ca_normalize.yaml +++ b/example-specs/task/nipype/freesurfer/ca_normalize.yaml @@ -157,11 +157,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"T1.mgz"' # type=file|default=: The input file for CANormalize - atlas: + atlas: '"atlas.nii.gz" # in practice use .gca atlases' # type=file|default=: The atlas file in gca format - transform: + transform: '"trans.mat" # in practice use .lta transforms' # type=file|default=: The transform file in lta format imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/ca_register.yaml b/example-specs/task/nipype/freesurfer/ca_register.yaml index c34ea647..69d511ba 100644 --- a/example-specs/task/nipype/freesurfer/ca_register.yaml +++ b/example-specs/task/nipype/freesurfer/ca_register.yaml @@ -160,7 +160,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"norm.mgz"' # type=file|default=: The input volume for CARegister out_file: '"talairach.m3z"' # type=file: The output file for CARegister diff --git a/example-specs/task/nipype/freesurfer/check_talairach_alignment.yaml b/example-specs/task/nipype/freesurfer/check_talairach_alignment.yaml index 6cf973ea..cabe72a5 100644 --- a/example-specs/task/nipype/freesurfer/check_talairach_alignment.yaml +++ b/example-specs/task/nipype/freesurfer/check_talairach_alignment.yaml @@ -124,7 +124,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"trans.mat"' # type=file|default=: specify the talairach.xfm file to check threshold: '0.005' # type=float|default=0.01: Talairach transforms for subjects with p-values <= T are considered as very unlikely default=0.010 diff --git a/example-specs/task/nipype/freesurfer/concatenate.yaml b/example-specs/task/nipype/freesurfer/concatenate.yaml index 6b55ebca..c3a56076 100644 --- a/example-specs/task/nipype/freesurfer/concatenate.yaml +++ b/example-specs/task/nipype/freesurfer/concatenate.yaml @@ -164,7 +164,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["cont1.nii", "cont2.nii"]' # type=inputmultiobject|default=[]: Individual volumes to be concatenated concatenated_file: '"bar.nii"' # type=file: Path/name of the output volume diff --git a/example-specs/task/nipype/freesurfer/concatenate_lta.yaml b/example-specs/task/nipype/freesurfer/concatenate_lta.yaml index ee794e25..c1537a30 100644 --- a/example-specs/task/nipype/freesurfer/concatenate_lta.yaml +++ b/example-specs/task/nipype/freesurfer/concatenate_lta.yaml @@ -204,7 +204,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_lta1: + in_lta1: '"lta1.lta"' # type=file|default=: maps some src1 to dst1 in_lta2: '"lta2.lta"' # type=traitcompound|default=None: maps dst1(src2) to dst2 diff --git a/example-specs/task/nipype/freesurfer/contrast.yaml b/example-specs/task/nipype/freesurfer/contrast.yaml index 3a915bfa..63402d44 100644 --- a/example-specs/task/nipype/freesurfer/contrast.yaml +++ b/example-specs/task/nipype/freesurfer/contrast.yaml @@ -168,17 +168,17 @@ doctests: # type=string|default='subject_id': Subject being processed hemisphere: '"lh"' # type=enum|default='lh'|allowed['lh','rh']: Hemisphere being processed - white: + white: '"lh.white" # doctest: +SKIP' # type=file|default=: Input file must be /surf/.white - thickness: + thickness: '"lh.thickness" # doctest: +SKIP' # type=file|default=: Input file must be /surf/?h.thickness - annotation: + annotation: '"../label/lh.aparc.annot" # doctest: +SKIP' # type=file|default=: Input annotation file must be /label/.aparc.annot - cortex: + cortex: '"../label/lh.cortex.label" # doctest: +SKIP' # type=file|default=: Input cortex label must be /label/.cortex.label - rawavg: + rawavg: '"../mri/rawavg.mgz" # doctest: +SKIP' # type=file|default=: Implicit input file mri/rawavg.mgz - orig: + orig: '"../mri/orig.mgz" # doctest: +SKIP' # type=file|default=: Implicit input file mri/orig.mgz imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/curvature.yaml b/example-specs/task/nipype/freesurfer/curvature.yaml index 0b1253cd..badc6f49 100644 --- a/example-specs/task/nipype/freesurfer/curvature.yaml +++ b/example-specs/task/nipype/freesurfer/curvature.yaml @@ -132,7 +132,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"lh.pial"' # type=file|default=: Input file for Curvature save: 'True' # type=bool|default=False: Save curvature files (will only generate screen output without this option) diff --git a/example-specs/task/nipype/freesurfer/curvature_stats.yaml b/example-specs/task/nipype/freesurfer/curvature_stats.yaml index 15332102..f7dc4828 100644 --- a/example-specs/task/nipype/freesurfer/curvature_stats.yaml +++ b/example-specs/task/nipype/freesurfer/curvature_stats.yaml @@ -183,11 +183,11 @@ doctests: # '.mock()' method of the corresponding class is used instead. hemisphere: '"lh"' # type=enum|default='lh'|allowed['lh','rh']: Hemisphere being processed - curvfile1: + curvfile1: '"lh.pial"' # type=file|default=: Input file for CurvatureStats - curvfile2: + curvfile2: '"lh.pial"' # type=file|default=: Input file for CurvatureStats - surface: + surface: '"lh.pial"' # type=file|default=: Specify surface file for CurvatureStats out_file: '"lh.curv.stats"' # type=file: Output curvature stats file diff --git a/example-specs/task/nipype/freesurfer/edit_w_mwith_aseg.yaml b/example-specs/task/nipype/freesurfer/edit_w_mwith_aseg.yaml index 132b6c56..e285c802 100644 --- a/example-specs/task/nipype/freesurfer/edit_w_mwith_aseg.yaml +++ b/example-specs/task/nipype/freesurfer/edit_w_mwith_aseg.yaml @@ -143,11 +143,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"T1.mgz"' # type=file|default=: Input white matter segmentation file - brain_file: + brain_file: '"norm.mgz"' # type=file|default=: Input brain/T1 file - seg_file: + seg_file: '"aseg.mgz"' # type=file|default=: Input presurf segmentation file out_file: '"wm.asegedit.mgz"' # type=file: Output edited WM file diff --git a/example-specs/task/nipype/freesurfer/em_register.yaml b/example-specs/task/nipype/freesurfer/em_register.yaml index 3b23bb7e..0c9faa40 100644 --- a/example-specs/task/nipype/freesurfer/em_register.yaml +++ b/example-specs/task/nipype/freesurfer/em_register.yaml @@ -150,9 +150,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"norm.mgz"' # type=file|default=: in brain volume - template: + template: '"aseg.mgz"' # type=file|default=: template gca out_file: '"norm_transform.lta"' # type=file: output transform diff --git a/example-specs/task/nipype/freesurfer/euler_number.yaml b/example-specs/task/nipype/freesurfer/euler_number.yaml index a753c37b..c0d1ee6f 100644 --- a/example-specs/task/nipype/freesurfer/euler_number.yaml +++ b/example-specs/task/nipype/freesurfer/euler_number.yaml @@ -115,7 +115,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"lh.pial"' # type=file|default=: Input file for EulerNumber imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/extract_main_component.yaml b/example-specs/task/nipype/freesurfer/extract_main_component.yaml index 039b28f5..e4f9a7f7 100644 --- a/example-specs/task/nipype/freesurfer/extract_main_component.yaml +++ b/example-specs/task/nipype/freesurfer/extract_main_component.yaml @@ -116,7 +116,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"lh.pial"' # type=file|default=: input surface file imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/fit_ms_params.yaml b/example-specs/task/nipype/freesurfer/fit_ms_params.yaml index 671df7de..14a4922e 100644 --- a/example-specs/task/nipype/freesurfer/fit_ms_params.yaml +++ b/example-specs/task/nipype/freesurfer/fit_ms_params.yaml @@ -136,7 +136,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["flash_05.mgz", "flash_30.mgz"]' # type=list|default=[]: list of FLASH images (must be in mgh format) out_dir: '"flash_parameters"' # type=directory|default=: directory to store output in diff --git a/example-specs/task/nipype/freesurfer/fix_topology.yaml b/example-specs/task/nipype/freesurfer/fix_topology.yaml index 9a52ec79..c66b8dc4 100644 --- a/example-specs/task/nipype/freesurfer/fix_topology.yaml +++ b/example-specs/task/nipype/freesurfer/fix_topology.yaml @@ -161,11 +161,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_orig: + in_orig: '"lh.orig" # doctest: +SKIP' # type=file|default=: Undocumented input file .orig - in_inflated: + in_inflated: '"lh.inflated" # doctest: +SKIP' # type=file|default=: Undocumented input file .inflated - sphere: + sphere: '"lh.qsphere.nofix" # doctest: +SKIP' # type=file|default=: Sphere input file hemisphere: '"lh"' # type=string|default='': Hemisphere being processed diff --git a/example-specs/task/nipype/freesurfer/fuse_segmentations.yaml b/example-specs/task/nipype/freesurfer/fuse_segmentations.yaml index e97b6641..10a30f9a 100644 --- a/example-specs/task/nipype/freesurfer/fuse_segmentations.yaml +++ b/example-specs/task/nipype/freesurfer/fuse_segmentations.yaml @@ -154,11 +154,11 @@ doctests: out_file: '"aseg.fused.mgz"' # type=file: output fused segmentation file # type=file|default=: output fused segmentation file - in_segmentations: + in_segmentations: '["aseg.mgz", "aseg.mgz"]' # type=inputmultiobject|default=[]: name of aseg file to use (default: aseg.mgz) must include the aseg files for all the given timepoints - in_segmentations_noCC: + in_segmentations_noCC: '["aseg.mgz", "aseg.mgz"]' # type=inputmultiobject|default=[]: name of aseg file w/o CC labels (default: aseg.auto_noCCseg.mgz) must include the corresponding file for all the given timepoints - in_norms: + in_norms: '["norm.mgz", "norm.mgz", "norm.mgz"]' # type=inputmultiobject|default=[]: -n - name of norm file to use (default: norm.mgs) must include the corresponding norm file for all given timepoints as well as for the current subject imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/glm_fit.yaml b/example-specs/task/nipype/freesurfer/glm_fit.yaml index b00e24ac..3d8ffc12 100644 --- a/example-specs/task/nipype/freesurfer/glm_fit.yaml +++ b/example-specs/task/nipype/freesurfer/glm_fit.yaml @@ -287,7 +287,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input 4D file one_sample: 'True' # type=bool|default=False: construct X and C as a one-sample group mean diff --git a/example-specs/task/nipype/freesurfer/gtmpvc.yaml b/example-specs/task/nipype/freesurfer/gtmpvc.yaml index a3a23ced..26856dbc 100644 --- a/example-specs/task/nipype/freesurfer/gtmpvc.yaml +++ b/example-specs/task/nipype/freesurfer/gtmpvc.yaml @@ -345,11 +345,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"sub-01_ses-baseline_pet.nii.gz"' # type=file|default=: input volume - source data to pvc - segmentation: + segmentation: '"gtmseg.mgz"' # type=file|default=: segfile : anatomical segmentation to define regions for GTM - reg_file: + reg_file: '"sub-01_ses-baseline_pet_mean_reg.lta"' # type=file|default=: LTA registration file that maps PET to anatomical pvc_dir: '"pvc"' # type=directory: output directory @@ -379,9 +379,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"sub-01_ses-baseline_pet.nii.gz"' # type=file|default=: input volume - source data to pvc - segmentation: + segmentation: '"gtmseg.mgz"' # type=file|default=: segfile : anatomical segmentation to define regions for GTM regheader: 'True' # type=bool|default=False: assume input and seg share scanner space diff --git a/example-specs/task/nipype/freesurfer/jacobian.yaml b/example-specs/task/nipype/freesurfer/jacobian.yaml index 9ef02846..5407295c 100644 --- a/example-specs/task/nipype/freesurfer/jacobian.yaml +++ b/example-specs/task/nipype/freesurfer/jacobian.yaml @@ -127,9 +127,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_origsurf: + in_origsurf: '"lh.pial"' # type=file|default=: Original surface - in_mappedsurf: + in_mappedsurf: '"lh.pial"' # type=file|default=: Mapped surface imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/label_2_annot.yaml b/example-specs/task/nipype/freesurfer/label_2_annot.yaml index ea454c64..c036e823 100644 --- a/example-specs/task/nipype/freesurfer/label_2_annot.yaml +++ b/example-specs/task/nipype/freesurfer/label_2_annot.yaml @@ -149,7 +149,7 @@ doctests: # type=string|default='subject_id': Subject name/ID in_labels: '["lh.aparc.label"]' # type=list|default=[]: List of input label files - orig: + orig: '"lh.pial"' # type=file|default=: implicit {hemisphere}.orig out_annot: '"test"' # type=string|default='': Name of the annotation to create diff --git a/example-specs/task/nipype/freesurfer/label_2_label.yaml b/example-specs/task/nipype/freesurfer/label_2_label.yaml index 7b76aa46..c4b87986 100644 --- a/example-specs/task/nipype/freesurfer/label_2_label.yaml +++ b/example-specs/task/nipype/freesurfer/label_2_label.yaml @@ -179,17 +179,17 @@ doctests: # type=enum|default='lh'|allowed['lh','rh']: Input hemisphere subject_id: '"10335"' # type=string|default='subject_id': Target subject - sphere_reg: + sphere_reg: '"lh.pial"' # type=file|default=: Implicit input .sphere.reg - white: + white: '"lh.pial"' # type=file|default=: Implicit input .white source_subject: '"fsaverage"' # type=string|default='': Source subject name - source_label: + source_label: '"lh-pial.stl"' # type=file|default=: Source label - source_white: + source_white: '"lh.pial"' # type=file|default=: Implicit input .white - source_sphere_reg: + source_sphere_reg: '"lh.pial"' # type=file|default=: Implicit input .sphere.reg imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/label_2_vol.yaml b/example-specs/task/nipype/freesurfer/label_2_vol.yaml index 37b2cdb4..3cd323a6 100644 --- a/example-specs/task/nipype/freesurfer/label_2_vol.yaml +++ b/example-specs/task/nipype/freesurfer/label_2_vol.yaml @@ -178,11 +178,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - label_file: + label_file: '"cortex.label"' # type=inputmultiobject|default=[]: list of label files - template_file: + template_file: '"structural.nii"' # type=file|default=: output template volume - reg_file: + reg_file: '"register.dat"' # type=file|default=: tkregister style matrix VolXYZ = R*LabelXYZ fill_thresh: '0.5' # type=range|default=0.0: thresh : between 0 and 1 diff --git a/example-specs/task/nipype/freesurfer/logan_ref.yaml b/example-specs/task/nipype/freesurfer/logan_ref.yaml index 2e4c1679..6e1ac42a 100644 --- a/example-specs/task/nipype/freesurfer/logan_ref.yaml +++ b/example-specs/task/nipype/freesurfer/logan_ref.yaml @@ -289,7 +289,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"tac.nii"' # type=file|default=: input 4D file logan: ("ref_tac.dat", "timing.dat", 2600) # type=tuple|default=(, , 0.0): RefTac TimeSec tstar : perform Logan kinetic modeling diff --git a/example-specs/task/nipype/freesurfer/make_surfaces.yaml b/example-specs/task/nipype/freesurfer/make_surfaces.yaml index af45fac6..a1f7cbb7 100644 --- a/example-specs/task/nipype/freesurfer/make_surfaces.yaml +++ b/example-specs/task/nipype/freesurfer/make_surfaces.yaml @@ -206,17 +206,17 @@ doctests: # type=enum|default='lh'|allowed['lh','rh']: Hemisphere being processed subject_id: '"10335"' # type=string|default='subject_id': Subject being processed - in_orig: + in_orig: '"lh.pial"' # type=file|default=: Implicit input file .orig - in_wm: + in_wm: '"wm.mgz"' # type=file|default=: Implicit input file wm.mgz - in_filled: + in_filled: '"norm.mgz"' # type=file|default=: Implicit input file filled.mgz - in_label: + in_label: '"aparc+aseg.nii"' # type=file|default=: Implicit input label/.aparc.annot - in_T1: + in_T1: '"T1.mgz"' # type=file|default=: Input brain or T1 file - orig_pial: + orig_pial: '"lh.pial"' # type=file|default=: Specify a pial surface to start with imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/mni_bias_correction.yaml b/example-specs/task/nipype/freesurfer/mni_bias_correction.yaml index 421d0f5c..93da1006 100644 --- a/example-specs/task/nipype/freesurfer/mni_bias_correction.yaml +++ b/example-specs/task/nipype/freesurfer/mni_bias_correction.yaml @@ -162,7 +162,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"norm.mgz"' # type=file|default=: input volume. Input can be any format accepted by mri_convert. iterations: '6' # type=int|default=4: Number of iterations to run nu_correct. Default is 4. This is the number of times that nu_correct is repeated (ie, using the output from the previous run as the input for the next). This is different than the -iterations option to nu_correct. diff --git a/example-specs/task/nipype/freesurfer/mr_is_ca_label.yaml b/example-specs/task/nipype/freesurfer/mr_is_ca_label.yaml index bc35ea7e..5f59bc82 100644 --- a/example-specs/task/nipype/freesurfer/mr_is_ca_label.yaml +++ b/example-specs/task/nipype/freesurfer/mr_is_ca_label.yaml @@ -184,15 +184,15 @@ doctests: # type=string|default='subject_id': Subject name or ID hemisphere: '"lh"' # type=enum|default='lh'|allowed['lh','rh']: Hemisphere ('lh' or 'rh') - canonsurf: + canonsurf: '"lh.pial"' # type=file|default=: Input canonical surface file - curv: + curv: '"lh.pial"' # type=file|default=: implicit input {hemisphere}.curv - sulc: + sulc: '"lh.pial"' # type=file|default=: implicit input {hemisphere}.sulc - classifier: + classifier: '"im1.nii" # in pracice, use .gcs extension' # type=file|default=: Classifier array input file - smoothwm: + smoothwm: '"lh.pial"' # type=file|default=: implicit input {hemisphere}.smoothwm imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/mr_is_calc.yaml b/example-specs/task/nipype/freesurfer/mr_is_calc.yaml index 28a9a0d7..d641db48 100644 --- a/example-specs/task/nipype/freesurfer/mr_is_calc.yaml +++ b/example-specs/task/nipype/freesurfer/mr_is_calc.yaml @@ -149,9 +149,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file1: + in_file1: '"lh.area" # doctest: +SKIP' # type=file|default=: Input file 1 - in_file2: + in_file2: '"lh.area.pial" # doctest: +SKIP' # type=file|default=: Input file 2 action: '"add"' # type=string|default='': Action to perform on input file(s) diff --git a/example-specs/task/nipype/freesurfer/mr_is_combine.yaml b/example-specs/task/nipype/freesurfer/mr_is_combine.yaml index 13d4483f..1bc45974 100644 --- a/example-specs/task/nipype/freesurfer/mr_is_combine.yaml +++ b/example-specs/task/nipype/freesurfer/mr_is_combine.yaml @@ -140,7 +140,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["lh.pial", "rh.pial"]' # type=list|default=[]: Two surfaces to be combined. out_file: '"bh.pial"' # type=file: Output filename. Combined surfaces from in_files. diff --git a/example-specs/task/nipype/freesurfer/mr_is_expand.yaml b/example-specs/task/nipype/freesurfer/mr_is_expand.yaml index ed473360..108e04f5 100644 --- a/example-specs/task/nipype/freesurfer/mr_is_expand.yaml +++ b/example-specs/task/nipype/freesurfer/mr_is_expand.yaml @@ -145,7 +145,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"lh.white"' # type=file|default=: Surface to expand out_name: '"graymid"' # type=str|default='expanded': Output surface file. If no path, uses directory of ``in_file``. If no path AND missing "lh." or "rh.", derive from ``in_file`` diff --git a/example-specs/task/nipype/freesurfer/mr_is_inflate.yaml b/example-specs/task/nipype/freesurfer/mr_is_inflate.yaml index ca9cbe35..7a75efd9 100644 --- a/example-specs/task/nipype/freesurfer/mr_is_inflate.yaml +++ b/example-specs/task/nipype/freesurfer/mr_is_inflate.yaml @@ -134,7 +134,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"lh.pial"' # type=file|default=: Input file for MRIsInflate no_save_sulc: 'True' # type=bool|default=False: Do not save sulc file as output diff --git a/example-specs/task/nipype/freesurfer/mri_convert.yaml b/example-specs/task/nipype/freesurfer/mri_convert.yaml index 462e6087..8bf361c9 100644 --- a/example-specs/task/nipype/freesurfer/mri_convert.yaml +++ b/example-specs/task/nipype/freesurfer/mri_convert.yaml @@ -311,7 +311,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: File to read/convert out_file: '"outfile.mgz"' # type=outputmultiobject: converted output file diff --git a/example-specs/task/nipype/freesurfer/mri_coreg.yaml b/example-specs/task/nipype/freesurfer/mri_coreg.yaml index bfed9616..44e2bb81 100644 --- a/example-specs/task/nipype/freesurfer/mri_coreg.yaml +++ b/example-specs/task/nipype/freesurfer/mri_coreg.yaml @@ -274,9 +274,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - source_file: + source_file: '"moving1.nii"' # type=file|default=: source file to be registered - reference_file: + reference_file: '"fixed1.nii"' # type=file|default=: reference (target) file subjects_dir: '"."' # type=directory|default=: FreeSurfer SUBJECTS_DIR @@ -291,7 +291,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - source_file: + source_file: '"moving1.nii"' # type=file|default=: source file to be registered subjects_dir: '"."' # type=directory|default=: FreeSurfer SUBJECTS_DIR diff --git a/example-specs/task/nipype/freesurfer/mri_fill.yaml b/example-specs/task/nipype/freesurfer/mri_fill.yaml index 840d1330..5147e808 100644 --- a/example-specs/task/nipype/freesurfer/mri_fill.yaml +++ b/example-specs/task/nipype/freesurfer/mri_fill.yaml @@ -142,7 +142,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"wm.mgz" # doctest: +SKIP' # type=file|default=: Input white matter file out_file: '"filled.mgz" # doctest: +SKIP' # type=file: Output file from MRIFill diff --git a/example-specs/task/nipype/freesurfer/mri_pretess.yaml b/example-specs/task/nipype/freesurfer/mri_pretess.yaml index 31d1f7d7..857e6651 100644 --- a/example-specs/task/nipype/freesurfer/mri_pretess.yaml +++ b/example-specs/task/nipype/freesurfer/mri_pretess.yaml @@ -145,9 +145,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_filled: + in_filled: '"wm.mgz"' # type=file|default=: filled volume, usually wm.mgz - in_norm: + in_norm: '"norm.mgz"' # type=file|default=: the normalized, brain-extracted T1w image. Usually norm.mgz nocorners: 'True' # type=bool|default=False: do not remove corner configurations in addition to edge ones. diff --git a/example-specs/task/nipype/freesurfer/mrtm.yaml b/example-specs/task/nipype/freesurfer/mrtm.yaml index 73756894..13bbc9b3 100644 --- a/example-specs/task/nipype/freesurfer/mrtm.yaml +++ b/example-specs/task/nipype/freesurfer/mrtm.yaml @@ -290,7 +290,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"tac.nii"' # type=file|default=: input 4D file mrtm1: ("ref_tac.dat", "timing.dat") # type=tuple|default=(, ): RefTac TimeSec : perform MRTM1 kinetic modeling diff --git a/example-specs/task/nipype/freesurfer/mrtm2.yaml b/example-specs/task/nipype/freesurfer/mrtm2.yaml index 4150c4b0..2a15b1d1 100644 --- a/example-specs/task/nipype/freesurfer/mrtm2.yaml +++ b/example-specs/task/nipype/freesurfer/mrtm2.yaml @@ -289,7 +289,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"tac.nii"' # type=file|default=: input 4D file mrtm2: ("ref_tac.dat", "timing.dat", 0.07872) # type=tuple|default=(, , 0.0): RefTac TimeSec k2prime : perform MRTM2 kinetic modeling diff --git a/example-specs/task/nipype/freesurfer/ms__lda.yaml b/example-specs/task/nipype/freesurfer/ms__lda.yaml index 5cb56ade..94af270a 100644 --- a/example-specs/task/nipype/freesurfer/ms__lda.yaml +++ b/example-specs/task/nipype/freesurfer/ms__lda.yaml @@ -164,7 +164,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. lda_labels: '[grey_label, white_label]' # type=list|default=[]: pair of class labels to optimize - label_file: + label_file: '"label.mgz"' # type=file|default=: filename of the label volume weight_file: '"weights.txt"' # type=file: @@ -178,7 +178,7 @@ doctests: # type=bool|default=False: Conform the input volumes (brain mask typically already conformed) use_weights: 'True' # type=bool|default=False: Use the weights from a previously generated weight file - images: + images: '["FLASH1.mgz", "FLASH2.mgz", "FLASH3.mgz"]' # type=inputmultiobject|default=[]: list of input FLASH images imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/normalize.yaml b/example-specs/task/nipype/freesurfer/normalize.yaml index 9fd7b237..704a66b1 100644 --- a/example-specs/task/nipype/freesurfer/normalize.yaml +++ b/example-specs/task/nipype/freesurfer/normalize.yaml @@ -139,7 +139,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"T1.mgz"' # type=file|default=: The input file for Normalize gradient: '1' # type=int|default=0: use max intensity/mm gradient g (default=1) diff --git a/example-specs/task/nipype/freesurfer/paint.yaml b/example-specs/task/nipype/freesurfer/paint.yaml index 37638240..b9eb0eac 100644 --- a/example-specs/task/nipype/freesurfer/paint.yaml +++ b/example-specs/task/nipype/freesurfer/paint.yaml @@ -142,9 +142,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_surf: + in_surf: '"lh.pial"' # type=file|default=: Surface file with grid (vertices) onto which the template data is to be sampled or 'painted' - template: + template: '"aseg.mgz"' # type=file|default=: Template file averages: '5' # type=int|default=0: Average curvature patterns diff --git a/example-specs/task/nipype/freesurfer/parcellation_stats.yaml b/example-specs/task/nipype/freesurfer/parcellation_stats.yaml index 94c84b8f..f9d82ab0 100644 --- a/example-specs/task/nipype/freesurfer/parcellation_stats.yaml +++ b/example-specs/task/nipype/freesurfer/parcellation_stats.yaml @@ -251,25 +251,25 @@ doctests: # type=string|default='subject_id': Subject being processed hemisphere: '"lh"' # type=enum|default='lh'|allowed['lh','rh']: Hemisphere being processed - wm: + wm: '"./../mri/wm.mgz" # doctest: +SKIP' # type=file|default=: Input file must be /mri/wm.mgz - transform: + transform: '"./../mri/transforms/talairach.xfm" # doctest: +SKIP' # type=file|default=: Input file must be /mri/transforms/talairach.xfm - brainmask: + brainmask: '"./../mri/brainmask.mgz" # doctest: +SKIP' # type=file|default=: Input file must be /mri/brainmask.mgz - aseg: + aseg: '"./../mri/aseg.presurf.mgz" # doctest: +SKIP' # type=file|default=: Input file must be /mri/aseg.presurf.mgz - ribbon: + ribbon: '"./../mri/ribbon.mgz" # doctest: +SKIP' # type=file|default=: Input file must be /mri/ribbon.mgz - lh_pial: + lh_pial: '"lh.pial" # doctest: +SKIP' # type=file|default=: Input file must be /surf/lh.pial - rh_pial: + rh_pial: '"lh.pial" # doctest: +SKIP' # type=file|default=: Input file must be /surf/rh.pial - lh_white: + lh_white: '"lh.white" # doctest: +SKIP' # type=file|default=: Input file must be /surf/lh.white - rh_white: + rh_white: '"rh.white" # doctest: +SKIP' # type=file|default=: Input file must be /surf/rh.white - thickness: + thickness: '"lh.thickness" # doctest: +SKIP' # type=file|default=: Input file must be /surf/?h.thickness surface: '"white"' # type=string|default='': Input surface (e.g. 'white') diff --git a/example-specs/task/nipype/freesurfer/recon_all.yaml b/example-specs/task/nipype/freesurfer/recon_all.yaml index 1e460283..703edf64 100644 --- a/example-specs/task/nipype/freesurfer/recon_all.yaml +++ b/example-specs/task/nipype/freesurfer/recon_all.yaml @@ -425,7 +425,7 @@ doctests: subjects_dir: '"."' # type=directory: Freesurfer subjects directory. # type=directory|default=: path to subjects directory - T1_files: + T1_files: '"structural.nii"' # type=inputmultiobject|default=[]: name of T1 file to process flags: '["-cw256", "-qcache"]' # type=inputmultiobject|default=[]: additional parameters @@ -476,7 +476,7 @@ doctests: subjects_dir: '"."' # type=directory: Freesurfer subjects directory. # type=directory|default=: path to subjects directory - T1_files: + T1_files: '"structural.nii"' # type=inputmultiobject|default=[]: name of T1 file to process hippocampal_subfields_T1: 'False' # type=bool|default=False: segment hippocampal subfields using input T1 scan diff --git a/example-specs/task/nipype/freesurfer/register.yaml b/example-specs/task/nipype/freesurfer/register.yaml index 8290675e..1d14a92d 100644 --- a/example-specs/task/nipype/freesurfer/register.yaml +++ b/example-specs/task/nipype/freesurfer/register.yaml @@ -152,13 +152,13 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_surf: + in_surf: '"lh.pial"' # type=file|default=: Surface to register, often {hemi}.sphere - in_smoothwm: + in_smoothwm: '"lh.pial"' # type=file|default=: Undocumented input file ${SUBJECTS_DIR}/surf/{hemisphere}.smoothwm - in_sulc: + in_sulc: '"lh.pial"' # type=file|default=: Undocumented mandatory input file ${SUBJECTS_DIR}/surf/{hemisphere}.sulc - target: + target: '"aseg.mgz"' # type=file|default=: The data to register to. In normal recon-all usage, this is a template file for average surface. out_file: '"lh.pial.reg"' # type=file: Output surface file to capture registration diff --git a/example-specs/task/nipype/freesurfer/register_av_ito_talairach.yaml b/example-specs/task/nipype/freesurfer/register_av_ito_talairach.yaml index fca71c21..2ea2a019 100644 --- a/example-specs/task/nipype/freesurfer/register_av_ito_talairach.yaml +++ b/example-specs/task/nipype/freesurfer/register_av_ito_talairach.yaml @@ -148,11 +148,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.mgz" # doctest: +SKIP' # type=file|default=: The input file - target: + target: '"mni305.cor.mgz" # doctest: +SKIP' # type=file|default=: The target file - vox2vox: + vox2vox: '"talsrcimg_to_structural_t4_vox2vox.txt" # doctest: +SKIP' # type=file|default=: The vox2vox file imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/relabel_hypointensities.yaml b/example-specs/task/nipype/freesurfer/relabel_hypointensities.yaml index 9446c782..00a02be9 100644 --- a/example-specs/task/nipype/freesurfer/relabel_hypointensities.yaml +++ b/example-specs/task/nipype/freesurfer/relabel_hypointensities.yaml @@ -141,13 +141,13 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - lh_white: + lh_white: '"lh.pial"' # type=file|default=: Implicit input file must be lh.white - rh_white: + rh_white: '"lh.pial"' # type=file|default=: Implicit input file must be rh.white surf_directory: '"."' # type=directory|default='.': Directory containing lh.white and rh.white - aseg: + aseg: '"aseg.mgz"' # type=file|default=: Input aseg file imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/remove_intersection.yaml b/example-specs/task/nipype/freesurfer/remove_intersection.yaml index 1fb2b8d7..5abc2285 100644 --- a/example-specs/task/nipype/freesurfer/remove_intersection.yaml +++ b/example-specs/task/nipype/freesurfer/remove_intersection.yaml @@ -120,7 +120,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"lh.pial"' # type=file|default=: Input file for RemoveIntersection imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/remove_neck.yaml b/example-specs/task/nipype/freesurfer/remove_neck.yaml index 39d7b5ca..b1678134 100644 --- a/example-specs/task/nipype/freesurfer/remove_neck.yaml +++ b/example-specs/task/nipype/freesurfer/remove_neck.yaml @@ -137,11 +137,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"norm.mgz"' # type=file|default=: Input file for RemoveNeck - transform: + transform: '"trans.mat"' # type=file|default=: Input transform file for RemoveNeck - template: + template: '"trans.mat"' # type=file|default=: Input template file for RemoveNeck imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/resample.yaml b/example-specs/task/nipype/freesurfer/resample.yaml index 15c6481c..4f716d5c 100644 --- a/example-specs/task/nipype/freesurfer/resample.yaml +++ b/example-specs/task/nipype/freesurfer/resample.yaml @@ -133,7 +133,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: file to resample resampled_file: '"resampled.nii"' # type=file: output filename diff --git a/example-specs/task/nipype/freesurfer/robust_register.yaml b/example-specs/task/nipype/freesurfer/robust_register.yaml index 11217c66..8c7146eb 100644 --- a/example-specs/task/nipype/freesurfer/robust_register.yaml +++ b/example-specs/task/nipype/freesurfer/robust_register.yaml @@ -222,9 +222,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - source_file: + source_file: '"structural.nii"' # type=file|default=: volume to be registered - target_file: + target_file: '"T1.nii"' # type=file|default=: target volume for the registration auto_sens: 'True' # type=bool|default=False: auto-detect good sensitivity diff --git a/example-specs/task/nipype/freesurfer/robust_template.yaml b/example-specs/task/nipype/freesurfer/robust_template.yaml index df30f9a5..03224b00 100644 --- a/example-specs/task/nipype/freesurfer/robust_template.yaml +++ b/example-specs/task/nipype/freesurfer/robust_template.yaml @@ -248,7 +248,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["structural.nii", "functional.nii"]' # type=inputmultiobject|default=[]: input movable volumes to be aligned to common mean/median template auto_detect_sensitivity: 'True' # type=bool|default=False: auto-detect good sensitivity (recommended for head or full brain scans) diff --git a/example-specs/task/nipype/freesurfer/sample_to_surface.yaml b/example-specs/task/nipype/freesurfer/sample_to_surface.yaml index 8480e191..d5660f11 100644 --- a/example-specs/task/nipype/freesurfer/sample_to_surface.yaml +++ b/example-specs/task/nipype/freesurfer/sample_to_surface.yaml @@ -232,9 +232,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - source_file: + source_file: '"cope1.nii.gz"' # type=file|default=: volume to sample values from - reg_file: + reg_file: '"register.dat"' # type=file|default=: source-to-reference registration file sampling_method: '"average"' # type=enum|default='point'|allowed['average','max','point']: how to sample -- at a point or at the max or average over a range diff --git a/example-specs/task/nipype/freesurfer/seg_stats.yaml b/example-specs/task/nipype/freesurfer/seg_stats.yaml index 1d776c13..a1c4acd3 100644 --- a/example-specs/task/nipype/freesurfer/seg_stats.yaml +++ b/example-specs/task/nipype/freesurfer/seg_stats.yaml @@ -242,7 +242,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. annot: ("PWS04", "lh", "aparc") # type=tuple|default=('', 'lh', ''): subject hemi parc : use surface parcellation - in_file: + in_file: '"functional.nii"' # type=file|default=: Use the segmentation to report stats on this volume subjects_dir: '"."' # type=directory|default=: subjects directory diff --git a/example-specs/task/nipype/freesurfer/seg_stats_recon_all.yaml b/example-specs/task/nipype/freesurfer/seg_stats_recon_all.yaml index 53f82c5c..f2b969ac 100644 --- a/example-specs/task/nipype/freesurfer/seg_stats_recon_all.yaml +++ b/example-specs/task/nipype/freesurfer/seg_stats_recon_all.yaml @@ -353,23 +353,23 @@ doctests: # type=file|default=: Segmentation stats summary table file subject_id: '"10335"' # type=string|default='subject_id': Subject id being processed - ribbon: + ribbon: '"wm.mgz"' # type=file|default=: Input file mri/ribbon.mgz - transform: + transform: '"trans.mat"' # type=file|default=: Input transform file - presurf_seg: + presurf_seg: '"wm.mgz"' # type=file|default=: Input segmentation volume - lh_orig_nofix: + lh_orig_nofix: '"lh.pial"' # type=file|default=: Input lh.orig.nofix - rh_orig_nofix: + rh_orig_nofix: '"lh.pial"' # type=file|default=: Input rh.orig.nofix - lh_pial: + lh_pial: '"lh.pial"' # type=file|default=: Input file must be /surf/lh.pial - rh_pial: + rh_pial: '"lh.pial"' # type=file|default=: Input file must be /surf/rh.pial - lh_white: + lh_white: '"lh.pial"' # type=file|default=: Input file must be /surf/lh.white - rh_white: + rh_white: '"lh.pial"' # type=file|default=: Input file must be /surf/rh.white empty: 'True' # type=bool|default=False: Report on segmentations listed in the color table diff --git a/example-specs/task/nipype/freesurfer/segment_cc.yaml b/example-specs/task/nipype/freesurfer/segment_cc.yaml index f02a9eb1..fc4cee03 100644 --- a/example-specs/task/nipype/freesurfer/segment_cc.yaml +++ b/example-specs/task/nipype/freesurfer/segment_cc.yaml @@ -154,9 +154,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"aseg.mgz"' # type=file|default=: Input aseg file to read from subjects directory - in_norm: + in_norm: '"norm.mgz"' # type=file|default=: Required undocumented input {subject}/mri/norm.mgz out_rotation: '"cc.lta"' # type=file: Output lta rotation file diff --git a/example-specs/task/nipype/freesurfer/segment_wm.yaml b/example-specs/task/nipype/freesurfer/segment_wm.yaml index c0de8828..6aa21efd 100644 --- a/example-specs/task/nipype/freesurfer/segment_wm.yaml +++ b/example-specs/task/nipype/freesurfer/segment_wm.yaml @@ -127,7 +127,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"norm.mgz"' # type=file|default=: Input file for SegmentWM out_file: '"wm.seg.mgz"' # type=file: Output white matter segmentation diff --git a/example-specs/task/nipype/freesurfer/smooth.yaml b/example-specs/task/nipype/freesurfer/smooth.yaml index 83884a4a..e41ed92d 100644 --- a/example-specs/task/nipype/freesurfer/smooth.yaml +++ b/example-specs/task/nipype/freesurfer/smooth.yaml @@ -155,12 +155,12 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: source volume smoothed_file: '"foo_out.nii"' # type=file: smoothed input volume # type=file|default=: output volume - reg_file: + reg_file: '"register.dat"' # type=file|default=: registers volume to surface anatomical surface_fwhm: '10' # type=range|default=0.0: surface FWHM in mm diff --git a/example-specs/task/nipype/freesurfer/sphere.yaml b/example-specs/task/nipype/freesurfer/sphere.yaml index 26e27c07..372e2600 100644 --- a/example-specs/task/nipype/freesurfer/sphere.yaml +++ b/example-specs/task/nipype/freesurfer/sphere.yaml @@ -130,7 +130,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"lh.pial"' # type=file|default=: Input file for Sphere imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/spherical_average.yaml b/example-specs/task/nipype/freesurfer/spherical_average.yaml index 0926bb7b..44ab8d71 100644 --- a/example-specs/task/nipype/freesurfer/spherical_average.yaml +++ b/example-specs/task/nipype/freesurfer/spherical_average.yaml @@ -176,7 +176,7 @@ doctests: # type=file|default=: Output filename in_average: '"."' # type=directory|default=: Average subject - in_surf: + in_surf: '"lh.pial"' # type=file|default=: Input surface file hemisphere: '"lh"' # type=enum|default='lh'|allowed['lh','rh']: Input hemisphere diff --git a/example-specs/task/nipype/freesurfer/surface_2_vol_transform.yaml b/example-specs/task/nipype/freesurfer/surface_2_vol_transform.yaml index 5490ad6b..60377be7 100644 --- a/example-specs/task/nipype/freesurfer/surface_2_vol_transform.yaml +++ b/example-specs/task/nipype/freesurfer/surface_2_vol_transform.yaml @@ -159,13 +159,13 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - source_file: + source_file: '"lh.cope1.mgz"' # type=file|default=: This is the source of the surface values - reg_file: + reg_file: '"register.mat"' # type=file|default=: tkRAS-to-tkRAS matrix (tkregister2 format) hemi: '"lh"' # type=str|default='': hemisphere of data - template_file: + template_file: '"cope1.nii.gz"' # type=file|default=: Output template volume subjects_dir: '"."' # type=str|default='': freesurfer subjects directory defaults to $SUBJECTS_DIR diff --git a/example-specs/task/nipype/freesurfer/surface_smooth.yaml b/example-specs/task/nipype/freesurfer/surface_smooth.yaml index eb3ac37a..de2587ae 100644 --- a/example-specs/task/nipype/freesurfer/surface_smooth.yaml +++ b/example-specs/task/nipype/freesurfer/surface_smooth.yaml @@ -157,7 +157,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"lh.cope1.mgz"' # type=file|default=: source surface file subject_id: '"subj_1"' # type=string|default='': subject id of surface file diff --git a/example-specs/task/nipype/freesurfer/synthesize_flash.yaml b/example-specs/task/nipype/freesurfer/synthesize_flash.yaml index 90691c2a..b33b3f0b 100644 --- a/example-specs/task/nipype/freesurfer/synthesize_flash.yaml +++ b/example-specs/task/nipype/freesurfer/synthesize_flash.yaml @@ -148,9 +148,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - t1_image: + t1_image: '"T1.mgz"' # type=file|default=: image of T1 values - pd_image: + pd_image: '"PD.mgz"' # type=file|default=: image of proton density values out_file: '"flash_30syn.mgz"' # type=file: synthesized FLASH acquisition diff --git a/example-specs/task/nipype/freesurfer/talairach_avi.yaml b/example-specs/task/nipype/freesurfer/talairach_avi.yaml index 33d19d45..7cb19425 100644 --- a/example-specs/task/nipype/freesurfer/talairach_avi.yaml +++ b/example-specs/task/nipype/freesurfer/talairach_avi.yaml @@ -137,7 +137,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"norm.mgz"' # type=file|default=: input volume out_file: '"trans.mat"' # type=file: The output transform for TalairachAVI diff --git a/example-specs/task/nipype/freesurfer/tkregister_2.yaml b/example-specs/task/nipype/freesurfer/tkregister_2.yaml index f1ae047f..1d91aab2 100644 --- a/example-specs/task/nipype/freesurfer/tkregister_2.yaml +++ b/example-specs/task/nipype/freesurfer/tkregister_2.yaml @@ -208,9 +208,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - moving_image: + moving_image: '"T1.mgz"' # type=file|default=: moving volume - target_image: + target_image: '"structural.nii"' # type=file|default=: target volume reg_header: 'True' # type=bool|default=False: compute regstration from headers @@ -228,9 +228,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - moving_image: + moving_image: '"epi.nii"' # type=file|default=: moving volume - fsl_in_matrix: + fsl_in_matrix: '"flirt.mat"' # type=file|default=: fsl-style registration input matrix imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/freesurfer/volume_mask.yaml b/example-specs/task/nipype/freesurfer/volume_mask.yaml index b911c25c..2fea6433 100644 --- a/example-specs/task/nipype/freesurfer/volume_mask.yaml +++ b/example-specs/task/nipype/freesurfer/volume_mask.yaml @@ -192,13 +192,13 @@ doctests: # type=int|default=0: Right white matter label right_ribbonlabel: '42' # type=int|default=0: Right cortical ribbon label - lh_pial: + lh_pial: '"lh.pial"' # type=file|default=: Implicit input left pial surface - rh_pial: + rh_pial: '"lh.pial"' # type=file|default=: Implicit input right pial surface - lh_white: + lh_white: '"lh.pial"' # type=file|default=: Implicit input left white matter surface - rh_white: + rh_white: '"lh.pial"' # type=file|default=: Implicit input right white matter surface subject_id: '"10335"' # type=string|default='subject_id': Subject being processed diff --git a/example-specs/task/nipype/freesurfer/watershed_skull_strip.yaml b/example-specs/task/nipype/freesurfer/watershed_skull_strip.yaml index eea42ee6..c5ff31ff 100644 --- a/example-specs/task/nipype/freesurfer/watershed_skull_strip.yaml +++ b/example-specs/task/nipype/freesurfer/watershed_skull_strip.yaml @@ -150,11 +150,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"T1.mgz"' # type=file|default=: input volume t1: 'True' # type=bool|default=False: specify T1 input volume (T1 grey value = 110) - transform: + transform: '"transforms/talairach_with_skull.lta"' # type=file|default=: undocumented out_file: '"brainmask.auto.mgz"' # type=file: skull stripped brain volume diff --git a/example-specs/task/nipype/fsl/apply_topup.yaml b/example-specs/task/nipype/fsl/apply_topup.yaml index 3763901a..07ed94f2 100644 --- a/example-specs/task/nipype/fsl/apply_topup.yaml +++ b/example-specs/task/nipype/fsl/apply_topup.yaml @@ -159,13 +159,13 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["epi.nii", "epi_rev.nii"]' # type=inputmultiobject|default=[]: name of file with images - encoding_file: + encoding_file: '"topup_encoding.txt"' # type=file|default=: name of text file with PE directions/times - in_topup_fieldcoef: + in_topup_fieldcoef: '"topup_fieldcoef.nii.gz"' # type=file|default=: topup file containing the field coefficients - in_topup_movpar: + in_topup_movpar: '"topup_movpar.txt"' # type=file|default=: topup movpar.txt file output_type: '"NIFTI_GZ"' # type=enum|default='NIFTI'|allowed['NIFTI','NIFTI_GZ','NIFTI_PAIR','NIFTI_PAIR_GZ']: FSL output type diff --git a/example-specs/task/nipype/fsl/b0_calc.yaml b/example-specs/task/nipype/fsl/b0_calc.yaml index bbcbe51b..a277b112 100644 --- a/example-specs/task/nipype/fsl/b0_calc.yaml +++ b/example-specs/task/nipype/fsl/b0_calc.yaml @@ -153,7 +153,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"tissue+air_map.nii"' # type=file|default=: filename of input image (usually a tissue/air segmentation) z_b0: '3.0' # type=float|default=1.0: Value for zeroth-order b0 field (z-component), in Tesla diff --git a/example-specs/task/nipype/fsl/bedpostx5.yaml b/example-specs/task/nipype/fsl/bedpostx5.yaml index 5ac61639..8708280e 100644 --- a/example-specs/task/nipype/fsl/bedpostx5.yaml +++ b/example-specs/task/nipype/fsl/bedpostx5.yaml @@ -214,13 +214,13 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - bvecs: + bvecs: '"bvecs"' # type=file|default=: b vectors file - bvals: + bvals: '"bvals"' # type=file|default=: b values file - dwi: + dwi: '"diffusion.nii"' # type=file|default=: diffusion weighted image data file - mask: + mask: '"mask.nii"' # type=file|default=: bet binary mask file n_fibres: '1' # type=range|default=2: Maximum number of fibres to fit in each voxel diff --git a/example-specs/task/nipype/fsl/bet.yaml b/example-specs/task/nipype/fsl/bet.yaml index b33740f2..9067cd21 100644 --- a/example-specs/task/nipype/fsl/bet.yaml +++ b/example-specs/task/nipype/fsl/bet.yaml @@ -190,7 +190,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: input file to skull strip frac: '0.7' # type=float|default=0.0: fractional intensity threshold diff --git a/example-specs/task/nipype/fsl/cluster.yaml b/example-specs/task/nipype/fsl/cluster.yaml index 3e651f7e..0a2b28a1 100644 --- a/example-specs/task/nipype/fsl/cluster.yaml +++ b/example-specs/task/nipype/fsl/cluster.yaml @@ -192,7 +192,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. threshold: '2.3' # type=float|default=0.0: threshold for input volume - in_file: + in_file: '"zstat1.nii.gz"' # type=file|default=: input volume out_localmax_txt_file: '"stats.txt"' # type=traitcompound|default=None: local maxima text file diff --git a/example-specs/task/nipype/fsl/convert_warp.yaml b/example-specs/task/nipype/fsl/convert_warp.yaml index 5fbd7a1a..e4d553f6 100644 --- a/example-specs/task/nipype/fsl/convert_warp.yaml +++ b/example-specs/task/nipype/fsl/convert_warp.yaml @@ -172,9 +172,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - warp1: + warp1: '"warpfield.nii"' # type=file|default=: Name of file containing initial warp-fields/coefficients (follows premat). This could e.g. be a fnirt-transform from a subjects structural scan to an average of a group of subjects. - reference: + reference: '"T1.nii"' # type=file|default=: Name of a file in target space of the full transform. relwarp: 'True' # type=bool|default=False: If set it indicates that the warps in --warp1/2 should be interpreted as relative. I.e. the values in --warp1/2 are displacements from the coordinates in the next space. diff --git a/example-specs/task/nipype/fsl/convert_xfm.yaml b/example-specs/task/nipype/fsl/convert_xfm.yaml index cfd52113..6cc22d8f 100644 --- a/example-specs/task/nipype/fsl/convert_xfm.yaml +++ b/example-specs/task/nipype/fsl/convert_xfm.yaml @@ -141,7 +141,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"flirt.mat"' # type=file|default=: input transformation matrix invert_xfm: 'True' # type=bool|default=False: invert input transformation diff --git a/example-specs/task/nipype/fsl/dti_fit.yaml b/example-specs/task/nipype/fsl/dti_fit.yaml index ee0044ec..19a0a2e4 100644 --- a/example-specs/task/nipype/fsl/dti_fit.yaml +++ b/example-specs/task/nipype/fsl/dti_fit.yaml @@ -189,15 +189,15 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - dwi: + dwi: '"diffusion.nii"' # type=file|default=: diffusion weighted image data file - bvecs: + bvecs: '"bvecs"' # type=file|default=: b vectors file - bvals: + bvals: '"bvals"' # type=file|default=: b values file base_name: '"TP"' # type=str|default='dtifit_': base_name that all output files will start with - mask: + mask: '"mask.nii"' # type=file|default=: bet binary mask file imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/fsl/dual_regression.yaml b/example-specs/task/nipype/fsl/dual_regression.yaml index 51b9625b..06b866e5 100644 --- a/example-specs/task/nipype/fsl/dual_regression.yaml +++ b/example-specs/task/nipype/fsl/dual_regression.yaml @@ -156,9 +156,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["functional.nii", "functional2.nii", "functional3.nii"]' # type=inputmultiobject|default=[]: List all subjects' preprocessed, standard-space 4D datasets - group_IC_maps_4D: + group_IC_maps_4D: '"allFA.nii"' # type=file|default=: 4D image containing spatial IC maps (melodic_IC) from the whole-group ICA analysis des_norm: 'False' # type=bool|default=True: Whether to variance-normalise the timecourses used as the stage-2 regressors; True is default and recommended diff --git a/example-specs/task/nipype/fsl/eddy.yaml b/example-specs/task/nipype/fsl/eddy.yaml index 1e4e2bd6..368ad6bc 100644 --- a/example-specs/task/nipype/fsl/eddy.yaml +++ b/example-specs/task/nipype/fsl/eddy.yaml @@ -333,9 +333,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"epi.nii"' # type=file|default=: File containing all the images to estimate distortions for - in_index: + in_index: '"epi_index.txt"' # type=file|default=: File containing indices for all volumes in --imain into --acqp and --topup imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item @@ -369,7 +369,7 @@ doctests: # type=int|default=0: Regularisation weight for slice-to-vol movement (reasonable range 1-10) slice2vol_interp: '"trilinear"' # type=enum|default='trilinear'|allowed['spline','trilinear']: Slice-to-vol interpolation model for estimation step - slice_order: + slice_order: '"epi_slspec.txt"' # type=file|default='': Name of text file completely specifying slice/group acquisition imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/fsl/eddy_correct.yaml b/example-specs/task/nipype/fsl/eddy_correct.yaml index bc60065e..6094f537 100644 --- a/example-specs/task/nipype/fsl/eddy_correct.yaml +++ b/example-specs/task/nipype/fsl/eddy_correct.yaml @@ -125,7 +125,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"diffusion.nii"' # type=file|default=: 4D input file out_file: '"diffusion_edc.nii"' # type=file|default=: 4D output file diff --git a/example-specs/task/nipype/fsl/eddy_quad.yaml b/example-specs/task/nipype/fsl/eddy_quad.yaml index 5889b2c3..916b9fd5 100644 --- a/example-specs/task/nipype/fsl/eddy_quad.yaml +++ b/example-specs/task/nipype/fsl/eddy_quad.yaml @@ -170,7 +170,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - param_file: + param_file: '"epi_acqp.txt"' # type=file|default=: File containing acquisition parameters output_dir: '"eddy_corrected.qc"' # type=str|default='': Output directory - default = '.qc' diff --git a/example-specs/task/nipype/fsl/epi_de_warp.yaml b/example-specs/task/nipype/fsl/epi_de_warp.yaml index 94e043d7..fd2d31c2 100644 --- a/example-specs/task/nipype/fsl/epi_de_warp.yaml +++ b/example-specs/task/nipype/fsl/epi_de_warp.yaml @@ -173,11 +173,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - epi_file: + epi_file: '"functional.nii"' # type=file|default=: EPI volume to unwarp - mag_file: + mag_file: '"magnitude.nii"' # type=file|default=: Magnitude file - dph_file: + dph_file: '"phase.nii"' # type=file|default=: Phase file assumed to be scaled from 0 to 4095 output_type: '"NIFTI_GZ"' # type=enum|default='NIFTI'|allowed['NIFTI','NIFTI_GZ','NIFTI_PAIR','NIFTI_PAIR_GZ']: FSL output type diff --git a/example-specs/task/nipype/fsl/epi_reg.yaml b/example-specs/task/nipype/fsl/epi_reg.yaml index 9f5ee15f..c187a6aa 100644 --- a/example-specs/task/nipype/fsl/epi_reg.yaml +++ b/example-specs/task/nipype/fsl/epi_reg.yaml @@ -207,19 +207,19 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - epi: + epi: '"epi.nii"' # type=file|default=: EPI image - t1_head: + t1_head: '"T1.nii"' # type=file|default=: wholehead T1 image - t1_brain: + t1_brain: '"T1_brain.nii"' # type=file|default=: brain extracted T1 image out_base: '"epi2struct"' # type=string|default='epi2struct': output base name - fmap: + fmap: '"fieldmap_phase_fslprepared.nii"' # type=file|default=: fieldmap image (in rad/s) - fmapmag: + fmapmag: '"fieldmap_mag.nii"' # type=file|default=: fieldmap magnitude image - wholehead - fmapmagbrain: + fmapmagbrain: '"fieldmap_mag_brain.nii"' # type=file|default=: fieldmap magnitude image - brain extracted echospacing: '0.00067' # type=float|default=0.0: Effective EPI echo spacing (sometimes called dwell time) - in seconds diff --git a/example-specs/task/nipype/fsl/extract_roi.yaml b/example-specs/task/nipype/fsl/extract_roi.yaml index 510f7faa..a58d7400 100644 --- a/example-specs/task/nipype/fsl/extract_roi.yaml +++ b/example-specs/task/nipype/fsl/extract_roi.yaml @@ -162,7 +162,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: anatfile # type=file|default=: input file roi_file: '"bar.nii"' # type=file: diff --git a/example-specs/task/nipype/fsl/fast.yaml b/example-specs/task/nipype/fsl/fast.yaml index 46f3df50..007930a3 100644 --- a/example-specs/task/nipype/fsl/fast.yaml +++ b/example-specs/task/nipype/fsl/fast.yaml @@ -184,7 +184,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '"structural.nii"' # type=inputmultiobject|default=[]: image, or multi-channel set of images, to be segmented out_basename: '"fast_"' # type=file|default=: base name of output files diff --git a/example-specs/task/nipype/fsl/find_the_biggest.yaml b/example-specs/task/nipype/fsl/find_the_biggest.yaml index 9a279486..5955dcbb 100644 --- a/example-specs/task/nipype/fsl/find_the_biggest.yaml +++ b/example-specs/task/nipype/fsl/find_the_biggest.yaml @@ -129,7 +129,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: ldir # type=list|default=[]: a list of input volumes or a singleMatrixFile out_file: '"biggestSegmentation"' # type=file: output file indexed in order of input files diff --git a/example-specs/task/nipype/fsl/flameo.yaml b/example-specs/task/nipype/fsl/flameo.yaml index a62ae479..2b735aaa 100644 --- a/example-specs/task/nipype/fsl/flameo.yaml +++ b/example-specs/task/nipype/fsl/flameo.yaml @@ -204,17 +204,17 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - cope_file: + cope_file: '"cope.nii.gz"' # type=file|default=: cope regressor data file - var_cope_file: + var_cope_file: '"varcope.nii.gz"' # type=file|default=: varcope weightings data file - cov_split_file: + cov_split_file: '"cov_split.mat"' # type=file|default=: ascii matrix specifying the groups the covariance is split into - design_file: + design_file: '"design.mat"' # type=file|default=: design matrix file - t_con_file: + t_con_file: '"design.con"' # type=file|default=: ascii matrix specifying t-contrasts - mask_file: + mask_file: '"mask.nii"' # type=file|default=: mask file run_mode: '"fe"' # type=enum|default='fe'|allowed['fe','flame1','flame12','ols']: inference to perform diff --git a/example-specs/task/nipype/fsl/flirt.yaml b/example-specs/task/nipype/fsl/flirt.yaml index 150b8331..5e39a3a1 100644 --- a/example-specs/task/nipype/fsl/flirt.yaml +++ b/example-specs/task/nipype/fsl/flirt.yaml @@ -263,9 +263,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"structural.nii"' # type=file|default=: input file - reference: + reference: '"mni.nii"' # type=file|default=: reference file output_type: '"NIFTI_GZ"' # type=enum|default='NIFTI'|allowed['NIFTI','NIFTI_GZ','NIFTI_PAIR','NIFTI_PAIR_GZ']: FSL output type diff --git a/example-specs/task/nipype/fsl/fugue.yaml b/example-specs/task/nipype/fsl/fugue.yaml index 560b3dce..20d9554f 100644 --- a/example-specs/task/nipype/fsl/fugue.yaml +++ b/example-specs/task/nipype/fsl/fugue.yaml @@ -327,11 +327,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"epi.nii"' # type=file|default=: filename of input volume - mask_file: + mask_file: '"epi_mask.nii"' # type=file|default=: filename for loading valid mask - shift_in_file: + shift_in_file: '"vsm.nii" # Previously computed with fugue as well' # type=file|default=: filename for reading pixel shift volume unwarp_direction: '"y"' # type=enum|default='x'|allowed['x','x-','y','y-','z','z-']: specifies direction of warping (default y) @@ -348,13 +348,13 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"epi.nii"' # type=file|default=: filename of input volume forward_warping: 'True' # type=bool|default=False: apply forward warping instead of unwarping - mask_file: + mask_file: '"epi_mask.nii"' # type=file|default=: filename for loading valid mask - shift_in_file: + shift_in_file: '"vsm.nii" # Previously computed with fugue as well' # type=file|default=: filename for reading pixel shift volume unwarp_direction: '"y"' # type=enum|default='x'|allowed['x','x-','y','y-','z','z-']: specifies direction of warping (default y) @@ -371,9 +371,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - phasemap_in_file: + phasemap_in_file: '"epi_phasediff.nii"' # type=file|default=: filename for input phase image - mask_file: + mask_file: '"epi_mask.nii"' # type=file|default=: filename for loading valid mask dwell_to_asym_ratio: (0.77e-3 * 3) / 2.46e-3 # type=float|default=0.0: set the dwell to asym time ratio diff --git a/example-specs/task/nipype/fsl/glm.yaml b/example-specs/task/nipype/fsl/glm.yaml index 1b61e1c9..532b6d85 100644 --- a/example-specs/task/nipype/fsl/glm.yaml +++ b/example-specs/task/nipype/fsl/glm.yaml @@ -214,9 +214,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input file name (text matrix or 3D/4D image file) - design: + design: '"maps.nii"' # type=file|default=: file name of the GLM design matrix (text time courses for temporal regression or an image file for spatial regression) output_type: '"NIFTI"' # type=enum|default='NIFTI'|allowed['NIFTI','NIFTI_GZ','NIFTI_PAIR','NIFTI_PAIR_GZ']: FSL output type diff --git a/example-specs/task/nipype/fsl/ica__aroma.yaml b/example-specs/task/nipype/fsl/ica__aroma.yaml index db48d378..2a980089 100644 --- a/example-specs/task/nipype/fsl/ica__aroma.yaml +++ b/example-specs/task/nipype/fsl/ica__aroma.yaml @@ -182,15 +182,15 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: volume to be denoised - mat_file: + mat_file: '"func_to_struct.mat"' # type=file|default=: path/name of the mat-file describing the affine registration (e.g. FSL FLIRT) of the functional data to structural space (.mat file) - fnirt_warp_file: + fnirt_warp_file: '"warpfield.nii"' # type=file|default=: File name of the warp-file describing the non-linear registration (e.g. FSL FNIRT) of the structural data to MNI152 space (.nii.gz) - motion_parameters: + motion_parameters: '"fsl_mcflirt_movpar.txt"' # type=file|default=: motion parameters file - mask: + mask: '"mask.nii.gz"' # type=file|default=: path/name volume mask denoise_type: '"both"' # type=enum|default='nonaggr'|allowed['aggr','both','no','nonaggr']: Type of denoising strategy: -no: only classification, no denoising -nonaggr (default): non-aggresssive denoising, i.e. partial component regression -aggr: aggressive denoising, i.e. full component regression -both: both aggressive and non-aggressive denoising (two outputs) diff --git a/example-specs/task/nipype/fsl/image_maths.yaml b/example-specs/task/nipype/fsl/image_maths.yaml index 57a2e7ee..f156853a 100644 --- a/example-specs/task/nipype/fsl/image_maths.yaml +++ b/example-specs/task/nipype/fsl/image_maths.yaml @@ -148,7 +148,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: anatfile # type=file|default=: op_string: '"-add 5"' # type=str|default='': string defining the operation, i. e. -add diff --git a/example-specs/task/nipype/fsl/image_stats.yaml b/example-specs/task/nipype/fsl/image_stats.yaml index 8fe54170..8c2f3fcb 100644 --- a/example-specs/task/nipype/fsl/image_stats.yaml +++ b/example-specs/task/nipype/fsl/image_stats.yaml @@ -133,7 +133,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: funcfile # type=file|default=: input file to generate stats of op_string: '"-M"' # type=str|default='': string defining the operation, options are applied in order, e.g. -M -l 10 -M will report the non-zero mean, apply a threshold and then report the new nonzero mean diff --git a/example-specs/task/nipype/fsl/inv_warp.yaml b/example-specs/task/nipype/fsl/inv_warp.yaml index ba8855c9..9151af0e 100644 --- a/example-specs/task/nipype/fsl/inv_warp.yaml +++ b/example-specs/task/nipype/fsl/inv_warp.yaml @@ -147,9 +147,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - warp: + warp: '"struct2mni.nii"' # type=file|default=: Name of file containing warp-coefficients/fields. This would typically be the output from the --cout switch of fnirt (but can also use fields, like the output from --fout). - reference: + reference: '"anatomical.nii"' # type=file|default=: Name of a file in target space. Note that the target space is now different from the target space that was used to create the --warp file. It would typically be the file that was specified with the --in argument when running fnirt. output_type: '"NIFTI_GZ"' # type=enum|default='NIFTI'|allowed['NIFTI','NIFTI_GZ','NIFTI_PAIR','NIFTI_PAIR_GZ']: FSL output type diff --git a/example-specs/task/nipype/fsl/max_image.yaml b/example-specs/task/nipype/fsl/max_image.yaml index 24d270c8..1d0e2d02 100644 --- a/example-specs/task/nipype/fsl/max_image.yaml +++ b/example-specs/task/nipype/fsl/max_image.yaml @@ -130,7 +130,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii" # doctest: +SKIP' # type=file|default=: image to operate on imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/fsl/mcflirt.yaml b/example-specs/task/nipype/fsl/mcflirt.yaml index 0b252239..f1ea002e 100644 --- a/example-specs/task/nipype/fsl/mcflirt.yaml +++ b/example-specs/task/nipype/fsl/mcflirt.yaml @@ -184,7 +184,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: timeseries to motion-correct cost: '"mutualinfo"' # type=enum|default='mutualinfo'|allowed['corratio','leastsquares','mutualinfo','normcorr','normmi','woods']: cost function to optimize diff --git a/example-specs/task/nipype/fsl/melodic.yaml b/example-specs/task/nipype/fsl/melodic.yaml index 9dca483d..05f40e83 100644 --- a/example-specs/task/nipype/fsl/melodic.yaml +++ b/example-specs/task/nipype/fsl/melodic.yaml @@ -272,7 +272,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. approach: '"tica"' # type=str|default='': approach for decomposition, 2D: defl, symm (default), 3D: tica (default), concat - in_files: + in_files: '["functional.nii", "functional2.nii", "functional3.nii"]' # type=inputmultiobject|default=[]: input file names (either single file name or a list) no_bet: 'True' # type=bool|default=False: switch off BET @@ -284,13 +284,13 @@ doctests: # type=float|default=0.0: threshold for Mixture Model based inference out_stats: 'True' # type=bool|default=False: output thresholded maps and probability maps - t_des: + t_des: '"timeDesign.mat"' # type=file|default=: design matrix across time-domain - t_con: + t_con: '"timeDesign.con"' # type=file|default=: t-contrast matrix across time-domain - s_des: + s_des: '"subjectDesign.mat"' # type=file|default=: design matrix across subject-domain - s_con: + s_con: '"subjectDesign.con"' # type=file|default=: t-contrast matrix across subject-domain out_dir: '"groupICA.out"' # type=directory: diff --git a/example-specs/task/nipype/fsl/merge.yaml b/example-specs/task/nipype/fsl/merge.yaml index 5602a912..dcf85517 100644 --- a/example-specs/task/nipype/fsl/merge.yaml +++ b/example-specs/task/nipype/fsl/merge.yaml @@ -142,7 +142,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: '["functional2.nii", "functional3.nii"]' # type=list|default=[]: dimension: '"t"' # type=enum|default='t'|allowed['a','t','x','y','z']: dimension along which to merge, optionally set tr input when dimension is t diff --git a/example-specs/task/nipype/fsl/motion_outliers.yaml b/example-specs/task/nipype/fsl/motion_outliers.yaml index d8e53c75..cca7ee4a 100644 --- a/example-specs/task/nipype/fsl/motion_outliers.yaml +++ b/example-specs/task/nipype/fsl/motion_outliers.yaml @@ -148,7 +148,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"epi.nii"' # type=file|default=: unfiltered 4D image imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/fsl/multi_image_maths.yaml b/example-specs/task/nipype/fsl/multi_image_maths.yaml index edf4250d..72a24c1b 100644 --- a/example-specs/task/nipype/fsl/multi_image_maths.yaml +++ b/example-specs/task/nipype/fsl/multi_image_maths.yaml @@ -143,11 +143,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: image to operate on op_string: '"-add %s -mul -1 -div %s"' # type=string|default='': python formatted string of operations to perform - operand_files: + operand_files: '["functional2.nii", "functional3.nii"]' # type=inputmultiobject|default=[]: list of file names to plug into op string out_file: '"functional4.nii"' # type=file: image written after calculations diff --git a/example-specs/task/nipype/fsl/percentile_image.yaml b/example-specs/task/nipype/fsl/percentile_image.yaml index fada70e4..01a51566 100644 --- a/example-specs/task/nipype/fsl/percentile_image.yaml +++ b/example-specs/task/nipype/fsl/percentile_image.yaml @@ -133,7 +133,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii" # doctest: +SKIP' # type=file|default=: image to operate on imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/fsl/prepare_fieldmap.yaml b/example-specs/task/nipype/fsl/prepare_fieldmap.yaml index 43346d59..90a0e12f 100644 --- a/example-specs/task/nipype/fsl/prepare_fieldmap.yaml +++ b/example-specs/task/nipype/fsl/prepare_fieldmap.yaml @@ -143,9 +143,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_phase: + in_phase: '"phase.nii"' # type=file|default=: Phase difference map, in SIEMENS format range from 0-4096 or 0-8192) - in_magnitude: + in_magnitude: '"magnitude.nii"' # type=file|default=: Magnitude difference map, brain extracted output_type: '"NIFTI_GZ"' # type=enum|default='NIFTI'|allowed['NIFTI','NIFTI_GZ','NIFTI_PAIR','NIFTI_PAIR_GZ']: FSL output type diff --git a/example-specs/task/nipype/fsl/prob_track_x.yaml b/example-specs/task/nipype/fsl/prob_track_x.yaml index 9929df40..03071e9a 100644 --- a/example-specs/task/nipype/fsl/prob_track_x.yaml +++ b/example-specs/task/nipype/fsl/prob_track_x.yaml @@ -249,13 +249,13 @@ doctests: # '.mock()' method of the corresponding class is used instead. samples_base_name: '"merged"' # type=str|default='merged': the rootname/base_name for samples files - mask: + mask: '"mask.nii"' # type=file|default=: bet binary mask file in diffusion space seed: '"MASK_average_thal_right.nii"' # type=traitcompound|default=None: seed volume(s), or voxel(s) or freesurfer label file mode: '"seedmask"' # type=enum|default='simple'|allowed['seedmask','simple','two_mask_symm']: options: simple (single seed voxel), seedmask (mask of seed voxels), twomask_symm (two bet binary masks) - xfm: + xfm: '"trans.mat"' # type=file|default=: transformation matrix taking seed space to DTI space (either FLIRT matrix or FNIRT warp_field) - default is identity n_samples: '3' # type=int|default=5000: number of samples - default=5000 @@ -267,13 +267,13 @@ doctests: # type=bool|default=True: outputs path distributions os2t: 'True' # type=bool|default=False: Outputs seeds to targets - target_masks: + target_masks: '["targets_MASK1.nii", "targets_MASK2.nii"]' # type=inputmultiobject|default=[]: list of target masks - required for seeds_to_targets classification - thsamples: + thsamples: '"merged_thsamples.nii"' # type=inputmultiobject|default=[]: - fsamples: + fsamples: '"merged_fsamples.nii"' # type=inputmultiobject|default=[]: - phsamples: + phsamples: '"merged_phsamples.nii"' # type=inputmultiobject|default=[]: out_dir: '"."' # type=directory|default=: directory to put the final volumes in diff --git a/example-specs/task/nipype/fsl/prob_track_x2.yaml b/example-specs/task/nipype/fsl/prob_track_x2.yaml index cd542edf..5b8140db 100644 --- a/example-specs/task/nipype/fsl/prob_track_x2.yaml +++ b/example-specs/task/nipype/fsl/prob_track_x2.yaml @@ -286,13 +286,13 @@ doctests: # '.mock()' method of the corresponding class is used instead. seed: '"seed_source.nii.gz"' # type=traitcompound|default=None: seed volume(s), or voxel(s) or freesurfer label file - thsamples: + thsamples: '"merged_th1samples.nii.gz"' # type=inputmultiobject|default=[]: - fsamples: + fsamples: '"merged_f1samples.nii.gz"' # type=inputmultiobject|default=[]: - phsamples: + phsamples: '"merged_ph1samples.nii.gz"' # type=inputmultiobject|default=[]: - mask: + mask: '"nodif_brain_mask.nii.gz"' # type=file|default=: bet binary mask file in diffusion space out_dir: '"."' # type=directory|default=: directory to put the final volumes in diff --git a/example-specs/task/nipype/fsl/proj_thresh.yaml b/example-specs/task/nipype/fsl/proj_thresh.yaml index 0db2ffe1..5ad55028 100644 --- a/example-specs/task/nipype/fsl/proj_thresh.yaml +++ b/example-specs/task/nipype/fsl/proj_thresh.yaml @@ -118,7 +118,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_files: + in_files: ldir # type=list|default=[]: a list of input volumes threshold: '3' # type=int|default=0: threshold indicating minimum number of seed voxels entering this mask region diff --git a/example-specs/task/nipype/fsl/randomise.yaml b/example-specs/task/nipype/fsl/randomise.yaml index 5de6f0ec..6b7ee93e 100644 --- a/example-specs/task/nipype/fsl/randomise.yaml +++ b/example-specs/task/nipype/fsl/randomise.yaml @@ -191,13 +191,13 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"allFA.nii"' # type=file|default=: 4D input file - mask: + mask: '"mask.nii"' # type=file|default=: mask image - tcon: + tcon: '"design.con"' # type=file|default=: t contrasts file - design_mat: + design_mat: '"design.mat"' # type=file|default=: design matrix file imports: *id001 # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/fsl/slice.yaml b/example-specs/task/nipype/fsl/slice.yaml index cc5e6135..92408dd8 100644 --- a/example-specs/task/nipype/fsl/slice.yaml +++ b/example-specs/task/nipype/fsl/slice.yaml @@ -119,7 +119,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"functional.nii"' # type=file|default=: input filename out_base_name: '"sl"' # type=str|default='': outputs prefix diff --git a/example-specs/task/nipype/fsl/smooth.yaml b/example-specs/task/nipype/fsl/smooth.yaml index 9c31083a..fd618dbe 100644 --- a/example-specs/task/nipype/fsl/smooth.yaml +++ b/example-specs/task/nipype/fsl/smooth.yaml @@ -199,7 +199,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. output_type: '"NIFTI_GZ"' # type=enum|default='NIFTI'|allowed['NIFTI','NIFTI_GZ','NIFTI_PAIR','NIFTI_PAIR_GZ']: FSL output type - in_file: + in_file: '"functional2.nii"' # type=file|default=: sigma: '8.0' # type=float|default=0.0: gaussian kernel sigma in mm (not voxels) @@ -216,7 +216,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. output_type: '"NIFTI_GZ"' # type=enum|default='NIFTI'|allowed['NIFTI','NIFTI_GZ','NIFTI_PAIR','NIFTI_PAIR_GZ']: FSL output type - in_file: + in_file: '"functional2.nii"' # type=file|default=: fwhm: '8.0' # type=float|default=0.0: gaussian kernel fwhm, will be converted to sigma in mm (not voxels) @@ -233,7 +233,7 @@ doctests: # '.mock()' method of the corresponding class is used instead. output_type: '"NIFTI_GZ"' # type=enum|default='NIFTI'|allowed['NIFTI','NIFTI_GZ','NIFTI_PAIR','NIFTI_PAIR_GZ']: FSL output type - in_file: + in_file: '"functional2.nii"' # type=file|default=: imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/fsl/smooth_estimate.yaml b/example-specs/task/nipype/fsl/smooth_estimate.yaml index 0acf4f9c..fdea86af 100644 --- a/example-specs/task/nipype/fsl/smooth_estimate.yaml +++ b/example-specs/task/nipype/fsl/smooth_estimate.yaml @@ -128,9 +128,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - zstat_file: + zstat_file: '"zstat1.nii.gz"' # type=file|default=: zstat image file - mask_file: + mask_file: '"mask.nii"' # type=file|default=: brain mask volume imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/fsl/text_2_vest.yaml b/example-specs/task/nipype/fsl/text_2_vest.yaml index b8f18b2d..05073070 100644 --- a/example-specs/task/nipype/fsl/text_2_vest.yaml +++ b/example-specs/task/nipype/fsl/text_2_vest.yaml @@ -124,7 +124,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"design.txt"' # type=file|default=: plain text file representing your design, contrast, or f-test matrix out_file: '"design.mat"' # type=file: matrix data in the format used by FSL tools diff --git a/example-specs/task/nipype/fsl/topup.yaml b/example-specs/task/nipype/fsl/topup.yaml index f6cb6c7f..128a7536 100644 --- a/example-specs/task/nipype/fsl/topup.yaml +++ b/example-specs/task/nipype/fsl/topup.yaml @@ -211,9 +211,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"b0_b0rev.nii"' # type=file|default=: name of 4D file with images - encoding_file: + encoding_file: '"topup_encoding.txt"' # type=file|default=: name of text file with PE directions/times output_type: '"NIFTI_GZ"' # type=enum|default='NIFTI'|allowed['NIFTI','NIFTI_GZ','NIFTI_PAIR','NIFTI_PAIR_GZ']: FSL output type diff --git a/example-specs/task/nipype/fsl/vec_reg.yaml b/example-specs/task/nipype/fsl/vec_reg.yaml index a17eea51..58dd74e1 100644 --- a/example-specs/task/nipype/fsl/vec_reg.yaml +++ b/example-specs/task/nipype/fsl/vec_reg.yaml @@ -160,11 +160,11 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"diffusion.nii"' # type=file|default=: filename for input vector or tensor field - affine_mat: + affine_mat: '"trans.mat"' # type=file|default=: filename for affine transformation matrix - ref_vol: + ref_vol: '"mni.nii"' # type=file|default=: filename for reference (target) volume out_file: '"diffusion_vreg.nii"' # type=file: path/name of filename for the registered vector or tensor field diff --git a/example-specs/task/nipype/fsl/vest_2_text.yaml b/example-specs/task/nipype/fsl/vest_2_text.yaml index d022a691..599cedc7 100644 --- a/example-specs/task/nipype/fsl/vest_2_text.yaml +++ b/example-specs/task/nipype/fsl/vest_2_text.yaml @@ -120,7 +120,7 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"design.mat"' # type=file|default=: matrix data stored in the format used by FSL tools imports: # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item diff --git a/example-specs/task/nipype/fsl/warp_points.yaml b/example-specs/task/nipype/fsl/warp_points.yaml index 3ddb40e9..2bb497cf 100644 --- a/example-specs/task/nipype/fsl/warp_points.yaml +++ b/example-specs/task/nipype/fsl/warp_points.yaml @@ -155,13 +155,13 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_coords: + in_coords: '"surf.txt"' # type=file|default=: filename of file containing coordinates - src_file: + src_file: '"epi.nii"' # type=file|default=: filename of source image - dest_file: + dest_file: '"T1.nii"' # type=file|default=: filename of destination image - warp_file: + warp_file: '"warpfield.nii"' # type=file|default=: filename of warpfield (e.g. intermediate2dest_warp.nii.gz) coord_mm: 'True' # type=bool|default=False: all coordinates in mm diff --git a/example-specs/task/nipype/fsl/warp_points_from_std.yaml b/example-specs/task/nipype/fsl/warp_points_from_std.yaml index 9642f878..fbf7d17c 100644 --- a/example-specs/task/nipype/fsl/warp_points_from_std.yaml +++ b/example-specs/task/nipype/fsl/warp_points_from_std.yaml @@ -148,13 +148,13 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_coords: + in_coords: '"surf.txt"' # type=file|default=: filename of file containing coordinates - img_file: + img_file: '"T1.nii"' # type=file|default=: filename of a destination image - std_file: + std_file: '"mni.nii"' # type=file|default=: filename of the image in standard space - warp_file: + warp_file: '"warpfield.nii"' # type=file|default=: filename of warpfield (e.g. intermediate2dest_warp.nii.gz) coord_mm: 'True' # type=bool|default=False: all coordinates in mm diff --git a/example-specs/task/nipype/fsl/warp_points_to_std.yaml b/example-specs/task/nipype/fsl/warp_points_to_std.yaml index 84f714e1..395843ca 100644 --- a/example-specs/task/nipype/fsl/warp_points_to_std.yaml +++ b/example-specs/task/nipype/fsl/warp_points_to_std.yaml @@ -161,13 +161,13 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_coords: + in_coords: '"surf.txt"' # type=file|default=: filename of file containing coordinates - img_file: + img_file: '"T1.nii"' # type=file|default=: filename of input image - std_file: + std_file: '"mni.nii"' # type=file|default=: filename of destination image - warp_file: + warp_file: '"warpfield.nii"' # type=file|default=: filename of warpfield (e.g. intermediate2dest_warp.nii.gz) coord_mm: 'True' # type=bool|default=False: all coordinates in mm diff --git a/example-specs/task/nipype/fsl/warp_utils.yaml b/example-specs/task/nipype/fsl/warp_utils.yaml index 558d63fa..3132d259 100644 --- a/example-specs/task/nipype/fsl/warp_utils.yaml +++ b/example-specs/task/nipype/fsl/warp_utils.yaml @@ -158,9 +158,9 @@ doctests: # dict[str, str] - name-value pairs for inputs to be provided to the doctest. # If the field is of file-format type and the value is None, then the # '.mock()' method of the corresponding class is used instead. - in_file: + in_file: '"warpfield.nii"' # type=file|default=: Name of file containing warp-coefficients/fields. This would typically be the output from the --cout switch of fnirt (but can also use fields, like the output from --fout). - reference: + reference: '"T1.nii"' # type=file|default=: Name of a file in target space. Note that the target space is now different from the target space that was used to create the --warp file. It would typically be the file that was specified with the --in argument when running fnirt. out_format: '"spline"' # type=enum|default='spline'|allowed['field','spline']: Specifies the output format. If set to field (default) the output will be a (4D) field-file. If set to spline the format will be a (4D) file of spline coefficients. diff --git a/nipype2pydra/pkg_gen/__init__.py b/nipype2pydra/pkg_gen/__init__.py index eafc1d4b..d7763002 100644 --- a/nipype2pydra/pkg_gen/__init__.py +++ b/nipype2pydra/pkg_gen/__init__.py @@ -549,7 +549,7 @@ def combine_types(type_, prev_type): DocTestGenerator, { "cmdline": cmdline, - "inputs": copy(test_inpts), + "inputs": copy(inpts), "imports": imports, "directive": directive, }, @@ -653,6 +653,11 @@ def copy_ignore(_, names): with open(pkg_dir / "README.rst", "w") as f: f.write(readme_rst) + with open(pkg_dir / "AUTHORS", "w") as f: + f.write("# Enter list of names and emails of contributors to this package") + + shutil.copyfile(TEMPLATES_DIR / "NOTICE", pkg_dir / "NOTICE") + fileformat_readme_path = related_pkgs_dir / "fileformats" / "README.rst" with open(fileformat_readme_path) as f: ff_readme_rst = f.read() @@ -678,6 +683,9 @@ def copy_ignore(_, names): with open(pkg_dir / "pyproject.toml", "w") as f: f.write(pyproject_toml) + for tool_path in (TEMPLATES_DIR / "tools").iterdir(): + shutil.copyfile(tool_path, pkg_dir / tool_path.name) + # Add "pydra.tasks..auto to gitignore" with open(pkg_dir / ".gitignore", "a") as f: f.write(f"\n/pydra/tasks/{pkg}/auto" f"\n/pydra/tasks/{pkg}/_version.py\n") @@ -720,7 +728,7 @@ def copy_ignore(_, names): continue with open(fspath) as f: contents = f.read() - contents = re.sub(r"\bCHANGEME\b", pkg, contents) + contents = contents.replace("CHANGEME", pkg) with open(fspath, "w") as f: f.write(contents) diff --git a/nipype2pydra/pkg_gen/resources/templates/NOTICE b/nipype2pydra/pkg_gen/resources/templates/NOTICE new file mode 100644 index 00000000..7ecb993d --- /dev/null +++ b/nipype2pydra/pkg_gen/resources/templates/NOTICE @@ -0,0 +1,6 @@ +Pydra-CHANGEME +Copyright 2024 Pydra Development Team + +The bases for the task interfaces defined in this package were semi-automatically converted +from Nipype interfaces (https://github.com/nipy/nipype) using the Nipype2Pydra tool +(https://github.com/nipype/nipype2pydra). diff --git a/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd.yaml b/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd.yaml index 783e364b..6c429808 100644 --- a/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd.yaml +++ b/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd.yaml @@ -9,31 +9,43 @@ name: CI/CD on: push: branches: [ main, develop ] - tags: [ '*' ] pull_request: branches: [ main, develop ] + release: + types: [published] repository_dispatch: - types: [create-release] + types: [create-post-release] + +env: + CHANGEME_version: + CHANGEME_install_dir: ${{ github.workspace }}/install jobs: nipype-conv: runs-on: ubuntu-latest steps: + - name: Checkout uses: actions/checkout@v4 - - name: Revert version to most recent tag on upstream update + + - name: Revert version to most recent version tag on upstream update if: github.event_name == 'repository_dispatch' - run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}') - - name: Set up Python ${{ matrix.python-version }} + run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}') + + - name: Set up Python uses: actions/setup-python@v5 + - name: Install build dependencies run: python -m pip install --upgrade pip + - name: Install requirements run: python -m pip install ./related-packages/fileformats -r ./nipype-auto-conv/requirements.txt + - name: Run automatic Nipype > Pydra conversion run: ./nipype-auto-conv/generate - - uses: actions/upload-artifact@v3 + + - uses: actions/upload-artifact@v4 with: name: converted-nipype path: pydra/tasks/CHANGEME/auto @@ -51,162 +63,160 @@ jobs: steps: - name: Checkout uses: actions/checkout@v4 - - name: Revert version to most recent tag on upstream update + + - name: Revert version to most recent version tag on upstream update if: github.event_name == 'repository_dispatch' - run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}') + run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}') + - name: Download tasks converted from Nipype - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: converted-nipype path: pydra/tasks/CHANGEME/auto + - name: Strip auto package from gitignore so it is included in package run: | sed -i '/\/pydra\/tasks\/CHANGEME\/auto/d' .gitignore + sed -i '/^_version.py/d' .gitignore + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} + - name: Install build dependencies run: | python -m pip install --upgrade pip + - name: Install Pydra run: | pushd $HOME pip install ${{ matrix.pydra }} popd python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + - name: Install task package run: | - pip install "./related-packages/fileformats[dev]" "related-packages/fileformats-extras[dev]" + pip install ${{ matrix.pip-flags }} "./related-packages/fileformats[dev]" + pip install ${{ matrix.pip-flags }} "related-packages/fileformats-extras[dev]" pip install ${{ matrix.pip-flags }} ".[dev]" python -c "import pydra.tasks.CHANGEME as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" python -c "import fileformats.medimage_CHANGEME as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" python -c "import fileformats.extras.medimage_CHANGEME as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - - fileformats-test: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ['3.8', '3.11'] - steps: - - uses: actions/checkout@v4 - - name: Revert version to most recent tag on upstream update - if: github.event_name == 'repository_dispatch' - run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}') - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - name: Install build dependencies - run: | - python -m pip install --upgrade pip - - name: Install task package - run: | - pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]" - python -c "import fileformats.medimage_CHANGEME as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - - name: Test fileformats with pytest - run: | - cd ./fileformats - pytest -sv --cov fileformats.medimage_CHANGEME --cov fileformats.extras.medimage_CHANGEME --cov-report xml . test: - needs: [nipype-conv, fileformats-test] - runs-on: ubuntu-22.04 + needs: [nipype-conv] + runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.8'] # '3.11' + python-version: ['3.8', '3.11'] steps: + - name: Removed unnecessary tools to free space run: | sudo rm -rf /usr/share/dotnet - sudo rm -rf "$AGENT_TOOLSDIRECTORY" - - name: Get Download cache Key - id: cache-key - run: echo "::set-output name=key::CHANGEME-linux-ubuntu22_amd64-7.4.1" - - name: Cache FreeSurfer - uses: actions/cache@v2 + sudo rm -rf "$AGENT_TOOLSDIRECTORY" + + - name: Checkout repo + uses: actions/checkout@v4 + + - name: Revert version to most recent version tag on Nipype or Nipype2Pydra update + if: github.event_name == 'repository_dispatch' + run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}') + + - name: Cache CHANGEME Install + id: cache-install + uses: actions/cache@v4 with: - path: $HOME/downloads/CHANGEME - key: ${{ steps.cache-key.outputs.key }} - restore-keys: | - CHANGEME-linux-ubuntu22_amd64-7.4.1 - - name: Download FreeSurfer - if: steps.cache-key.outputs.key != steps.cache-hit.outputs.key - run: | - mkdir -p $HOME/downloads/CHANGEME - curl -s -o $HOME/downloads/CHANGEME/CHANGEME-linux-ubuntu22_amd64-7.4.1.tar.gz https://surfer.nmr.mgh.harvard.edu/pub/dist/CHANGEME/7.4.1/CHANGEME-linux-ubuntu22_amd64-7.4.1.tar.gz - shell: bash - - name: Install Freesurfer - env: - FREESURFER_LICENCE: ${{ secrets.FREESURFER_LICENCE }} + path: ${{ env.CHANGEME_install_dir }} + key: CHANGEME-${{ env.CHANGEME_version }}-${{ runner.os }} + + - name: Install CHANGEME Package + if: steps.cache-install.outputs.cache-hit != 'true' run: | - pushd $HOME/downloads/CHANGEME - tar -zxpf CHANGEME-linux-ubuntu22_amd64-7.4.1.tar.gz - mv CHANGEME $HOME/ - popd - export FREESURFER_HOME=$HOME/CHANGEME - source $FREESURFER_HOME/SetUpFreeSurfer.sh - echo $FREESURFER_LICENCE > $FREESURFER_HOME/license.txt - export PATH=$FREESURFER_HOME/bin:$PATH - - uses: actions/checkout@v4 - - name: Revert version to most recent tag on upstream update - if: github.event_name == 'repository_dispatch' - run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}') + echo "NOT IMPLEMENTED YET (install at CHANGEME_install_dir: $CHANGEME_install_dir)" + exit 1 # This is a placeholder, replace this line and the one above with the installation procedure + echo "PATH=${{ env.CHANGEME_install_dir }}/bin:$PATH" >> $GITHUB_ENV + - name: Download tasks converted from Nipype - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: converted-nipype path: pydra/tasks/CHANGEME/auto + + - name: Show the contents of the auto-generated tasks + run: tree pydra + - name: Strip auto package from gitignore so it is included in package run: | - sed -i '/\/src\/pydra\/tasks\/CHANGEME\/auto/d' .gitignore + sed -i '/\/pydra\/tasks\/CHANGEME\/auto/d' .gitignore + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} + - name: Install build dependencies run: | python -m pip install --upgrade pip + - name: Install task package run: | pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]" python -c "import pydra.tasks.CHANGEME as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + - name: Test with pytest - run: | - pytest -sv --doctest-modules ./pydra/tasks/CHANGEME \ - --cov pydra.tasks.CHANGEME --cov-report xml - - uses: codecov/codecov-action@v3 + run: >- + pytest -sv + ./pydra/tasks/CHANGEME + ./related-packages/fileformats + ./related-packages/fileformats-extras + --cov pydra.tasks.CHANGEME + --cov fileformats.medimage_CHANGEME + --cov fileformats.extras.medimage_CHANGEME + --cov-report xml + + - name: Upload to CodeCov + uses: codecov/codecov-action@v3 if: ${{ always() }} with: - files: coverage.xml,./fileformats/coverage.xml + files: coverage.xml name: pydra-CHANGEME + deploy-fileformats: needs: [devcheck, test] runs-on: ubuntu-latest steps: + - uses: actions/checkout@v4 with: submodules: recursive - fetch-depth: 0 + fetch-depth: 0 + - name: Set up Python uses: actions/setup-python@v5 with: python-version: '3.11' + - name: Install build tools run: python -m pip install build twine + - name: Build source and wheel distributions run: python -m build ./related-packages/fileformats + - name: Check distributions run: twine check ./related-packages/fileformats/dist/* + - name: Check for PyPI token on tag id: deployable - if: (github.event_name == 'push' && startsWith(github.ref, 'refs/tags')) || github.event_name == 'repository_dispatch' + if: github.event_name == 'release' || github.event_name == 'repository_dispatch' env: PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}" run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi + - name: Upload to PyPI if: steps.deployable.outputs.DEPLOY uses: pypa/gh-action-pypi-publish@release/v1 @@ -219,26 +229,33 @@ jobs: needs: [deploy-fileformats] runs-on: ubuntu-latest steps: + - uses: actions/checkout@v4 with: submodules: recursive - fetch-depth: 0 + fetch-depth: 0 + - name: Set up Python uses: actions/setup-python@v5 with: python-version: '3.11' + - name: Install build tools run: python -m pip install build twine + - name: Build source and wheel distributions run: python -m build ./related-packages/fileformats-extras + - name: Check distributions run: twine check ./related-packages/fileformats-extras/dist/* + - name: Check for PyPI token on tag id: deployable - if: (github.event_name == 'push' && startsWith(github.ref, 'refs/tags')) || github.event_name == 'repository_dispatch' + if: github.event_name == 'release' || github.event_name == 'repository_dispatch' env: PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}" run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi + - name: Upload to PyPI if: steps.deployable.outputs.DEPLOY uses: pypa/gh-action-pypi-publish@release/v1 @@ -248,58 +265,142 @@ jobs: packages-dir: ./related-packages/fileformats-extras/dist deploy: - needs: [deploy-fileformats-extras] + needs: [nipype-conv, test, deploy-fileformats, deploy-fileformats-extras] runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + + - name: Checkout repository + uses: actions/checkout@v4 with: submodules: recursive fetch-depth: 0 + + - name: Set up Git user + run: | + git config --local user.email "action@github.com" + git config --local user.name "GitHub Action" + + - name: Get latest version tag + id: latest_tag + run: | + git fetch --tags + echo "TAG=$(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')" >> $GITHUB_OUTPUT + + - name: Revert to latest tag + if: github.event_name == 'repository_dispatch' + run: git checkout ${{ steps.latest_tag.outputs.TAG }} + - name: Download tasks converted from Nipype - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: converted-nipype path: pydra/tasks/CHANGEME/auto - - name: Tag release with a post-release based on Nipype and Nipype2Pydra versions - if: github.event_name == 'repository_dispatch' - run: | - TAG=$(git tag -l | tail -n 1 | awk -F post '{print $1}') - POST=$(python -c "from pydra.tasks.CHANGEME.auto._version import *; print(post_release)") - git checkout $TAG - git add -f pydra/tasks/CHANGEME/auto/_version.py - git commit -am"added auto-generated version to make new tag for package version" - git tag ${TAG}post${POST} + + - name: Show the contents of the auto-generated tasks + run: tree pydra + - name: Set up Python uses: actions/setup-python@v5 with: python-version: '3.11' + - name: Install build tools run: python -m pip install build twine + - name: Strip auto package from gitignore so it is included in package run: | sed -i '/\/pydra\/tasks\/CHANGEME\/auto/d' .gitignore + cat .gitignore + + - name: Install task package to calculate post-release tag + run: | + pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]" + + - name: Generate post-release tag based on Nipype and Nipype2Pydra versions + id: post_release_tag + run: | + POST=$(python -c "from pydra.tasks.CHANGEME.auto._version import *; print(post_release)") + echo "TAG=${{ steps.latest_tag.outputs.TAG }}post${POST}" >> $GITHUB_OUTPUT + + - name: Add auto directory to git repo + if: github.event_name == 'release' || github.event_name == 'repository_dispatch' + run: | + git add pydra/tasks/CHANGEME/auto + git commit -am"added auto-generated version to make new tag for package version" + git status + + - name: Overwrite the tag of release event with latest commit (i.e. including the auto directory) + if: github.event_name == 'release' + run: | + git tag -d ${{ steps.latest_tag.outputs.TAG }}; + git tag ${{ steps.latest_tag.outputs.TAG }}; + + - name: Tag repo with the post-release + if: github.event_name == 'repository_dispatch' + run: git tag ${{ steps.post_release_tag.outputs.TAG }} + - name: Build source and wheel distributions run: python -m build . + - name: Check distributions run: twine check dist/* - - uses: actions/upload-artifact@v3 + + - uses: actions/upload-artifact@v4 with: name: distributions path: dist/ + - name: Check for PyPI token on tag id: deployable - if: (github.event_name == 'push' && startsWith(github.ref, 'refs/tags')) || github.event_name == 'repository_dispatch' + if: github.event_name == 'release' || github.event_name == 'repository_dispatch' env: PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}" run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi + - name: Upload to PyPI if: steps.deployable.outputs.DEPLOY uses: pypa/gh-action-pypi-publish@release/v1 with: user: __token__ - password: ${{ secrets.PYPI_API_TOKEN }} + password: ${{ secrets.PYPI_API_TOKEN }} + + - name: Create post-release release for releases triggered by nipype2pydra dispatches + if: steps.deployable.outputs.DEPLOY && github.event_name == 'repository_dispatch' + uses: actions/create-release@v1 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token + with: + tag_name: ${{ steps.post_release_tag.outputs.TAG }} + release_name: Release ${{ steps.post_release_tag.outputs.TAG }} + draft: false + prerelease: false + + + report_progress: + needs: [deploy] + runs-on: ubuntu-latest + steps: + + - name: Generate progress report + id: generate-report + run: | + tools/report_progress.py outputs/progress-report.json + echo "progress_report=$(cat outputs/progress-report.json)" >> $GITHUB_OUTPUT + + - name: Report progress to Nipype2Pydra repo + if: github.event_name == 'release' || github.event_name == 'repository_dispatch' + run: >- + curl -XPOST -u "${{ env.POST_RELEASE_PAT }}" -H "Accept: application/vnd.github.everest-preview+json" + "https://api.github.com/repos/nipype/pydra-CHANGEME/dispatches" + -d '{ + "event_type": "progress-report", + "client_payload": ${{ steps.generate-report.output.progress_report }} + }' + env: + PAT: ${{ env.PROGRESS_REPORT_PAT }} + # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets. # Secrets are not accessible in the if: condition [0], so set an output variable [1] # [0] https://github.community/t/16928 -# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter \ No newline at end of file +# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter diff --git a/nipype2pydra/pkg_gen/resources/templates/nipype-auto-convert-requirements.txt b/nipype2pydra/pkg_gen/resources/templates/nipype-auto-convert-requirements.txt index 9048c8e7..52d3e4a0 100644 --- a/nipype2pydra/pkg_gen/resources/templates/nipype-auto-convert-requirements.txt +++ b/nipype2pydra/pkg_gen/resources/templates/nipype-auto-convert-requirements.txt @@ -1,6 +1,7 @@ black attrs>=22.1.0 nipype +tqdm pydra PyYAML>=6.0 fileformats >=0.8 diff --git a/nipype2pydra/pkg_gen/resources/templates/nipype-auto-convert.py b/nipype2pydra/pkg_gen/resources/templates/nipype-auto-convert.py index 32377c96..19fc2929 100644 --- a/nipype2pydra/pkg_gen/resources/templates/nipype-auto-convert.py +++ b/nipype2pydra/pkg_gen/resources/templates/nipype-auto-convert.py @@ -6,6 +6,7 @@ import shutil from importlib import import_module import yaml +from tqdm import tqdm import nipype import nipype2pydra.utils from nipype2pydra.task import get_converter @@ -36,7 +37,9 @@ shutil.rmtree(auto_dir) all_interfaces = [] -for fspath in sorted(SPECS_DIR.glob("**/*.yaml")): +for fspath in tqdm( + sorted(SPECS_DIR.glob("**/*.yaml")), "converting interfaces from Nipype to Pydra" +): with open(fspath) as f: spec = yaml.load(f, Loader=yaml.SafeLoader) @@ -70,7 +73,9 @@ """ ) -auto_init += "\n\n__all__ = [\n" + "\n".join(f" \"{i}\"," for i in all_interfaces) + "\n]\n" +auto_init += ( + "\n\n__all__ = [\n" + "\n".join(f' "{i}",' for i in all_interfaces) + "\n]\n" +) with open(PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto" / "__init__.py", "w") as f: f.write(auto_init) diff --git a/nipype2pydra/pkg_gen/resources/templates/tools/report_progress.py b/nipype2pydra/pkg_gen/resources/templates/tools/report_progress.py new file mode 100755 index 00000000..1fc07674 --- /dev/null +++ b/nipype2pydra/pkg_gen/resources/templates/tools/report_progress.py @@ -0,0 +1,31 @@ +#!/usr/bin/env python3 +from pathlib import Path +import json +import yaml +import click + + +@click.command +@click.argument( + "out_json_path", + type=click.Path(path_type=Path), + help="The output path to save the report", +) +def report_progress(out_json_path: Path): + + out_json_path.parent.mkdir(exist_ok=True, parents=True) + + SPECS_DIR = Path(__file__).parent / "nipype-auto-conv" / "specs" + + report = {} + + for spec_path in SPECS_DIR.glob("*.yaml"): + with open(spec_path) as f: + spec = yaml.load(f, Loader=yaml.SafeLoader) + + report[spec["task_name"]] = { + n: not s["xfail"] for n, s in spec["tests"].items() + } + + with open(out_json_path, "w") as f: + json.dump(report, f) diff --git a/nipype2pydra/task/base.py b/nipype2pydra/task/base.py index 9a610866..fdc718c2 100644 --- a/nipype2pydra/task/base.py +++ b/nipype2pydra/task/base.py @@ -911,7 +911,23 @@ def create_doctests(self, input_fields, nonstd_types): else: val = attrs.NOTHING else: - if isinstance(val, str): + if is_fileset(tp): + val = f"{tp.__name__}.mock({val})" + elif ty.get_origin(tp) is list and is_fileset(ty.get_args(tp)[0]): + try: + val = eval(val) + except Exception: + pass + else: + val = ( + "[" + + ", ".join( + f'{ty.get_args(tp)[0].__name__}.mock("{v}")' + for v in val + ) + + "]" + ) + elif tp is str and not (val.startswith("'") or val.startswith('"')): val = f'"{val}"' if val is None and is_fileset(tp): val = f"{tp.__name__}.mock()" diff --git a/nipype2pydra/task/tests/test_task.py b/nipype2pydra/task/tests/test_task.py index 7de438f3..6df5b7f5 100644 --- a/nipype2pydra/task/tests/test_task.py +++ b/nipype2pydra/task/tests/test_task.py @@ -2,10 +2,16 @@ import yaml import pytest import logging -from nipype2pydra.utils import show_cli_trace +import io +import contextlib from traceback import format_exc from nipype2pydra.cli.task import task as task_cli -from nipype2pydra.utils import add_to_sys_path, add_exc_note, INBUILT_NIPYPE_TRAIT_NAMES +from nipype2pydra.utils import ( + add_to_sys_path, + add_exc_note, + INBUILT_NIPYPE_TRAIT_NAMES, + show_cli_trace, +) from conftest import EXAMPLE_TASKS_DIR @@ -120,6 +126,23 @@ def test_task_conversion(task_spec_file, cli_runner, work_dir, gen_test_conftest ) ) + # Run doctests + # logging.info("Running doctests for %s", output_module_path) + # with add_to_sys_path(pkg_root): + # with contextlib.redirect_stdout(io.StringIO()) as f: + # exit_code = pytest.main( + # [ + # str( + # pkg_root.joinpath( + # *output_module_path.split(".") + # ).with_suffix(".py") + # ), + # "--doctest-modules", + # "--ignore-glob=test_*.py", + # ] + # ) + + # assert not exit_code, f.getvalue() # tests_fspath = pkg_root.joinpath(*output_module_path.split(".")).parent / "tests" # # logging.info("Running generated tests for %s", output_module_path)