[FIX] Change check on type in converter NIFD #1229
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* add glossary page with a few examples * add some cross-references to the added terms as a demo * Add some more
…eprocessing utils (aramis-lab#1116) * Move DWI specific functions from filemanip utils to dwi utils preproc pipeline utils * Fix typing that works only for Python >= 3.10 * Clean api
Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.2.0 to 10.3.0. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@10.2.0...10.3.0) --- updated-dependencies: - dependency-name: pillow dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* add definition for FWHM * add link for FWHM
* add definition for SUVR in glossary and link in ML_prepareSVM description * Update docs/glossary.md --------- Co-authored-by: Gensollen <[email protected]>
…ramis-lab#1127) * Check that BIDS folders have a dataset_description.json file * make the _check_bids_is_not_empty function a bit more robust
* Use an enum for the study names * update unit tests * forgot one
Bumps [idna](https://github.com/kjd/idna) from 3.6 to 3.7. - [Release notes](https://github.com/kjd/idna/releases) - [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst) - [Commits](kjd/idna@v3.6...v3.7) --- updated-dependencies: - dependency-name: idna dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* refactor freesurfer pipelines * add forgotten cli * use absolute imports in task definitions * allow string or Path for get_subject_id * fix folder creation in init_input_node
* run linter on maint branches * run unit tests on maint branches * run converter non regression tests on maint branches * run instantiation tests on maint branches
…lab#1153) * move bids version definition * update unit tests
* update OASIS website URL * Apply suggestions from code review
aramis-lab#1159) * Wrong Processed sequence --> Results: Impossible to make bids of FDG PET Uniform (does not find it) * Linter exception * Linter word-list exception update * Update clinica/iotools/converters/adni_to_bids/adni_modalities/adni_fdg_pet.py Co-authored-by: Gensollen <[email protected]> * Update pyproject.toml Co-authored-by: Gensollen <[email protected]> * Update clinica/iotools/converters/adni_to_bids/adni_modalities/adni_fdg_pet.py Co-authored-by: Gensollen <[email protected]> * Update clinica/iotools/converters/adni_to_bids/adni_modalities/adni_fdg_pet.py * try using a text file for ignoring words * remove useless codespell:ignore * sort ignore words --------- Co-authored-by: Gensollen <[email protected]>
* Unify DatasetType class * Fix unit test match
Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.66.1 to 4.66.3. - [Release notes](https://github.com/tqdm/tqdm/releases) - [Commits](tqdm/tqdm@v4.66.1...v4.66.3) --- updated-dependencies: - dependency-name: tqdm dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…line (aramis-lab#1194) * fix typo in github context variable * split between test and doc runners for Linux
…b#1190) * Preliminary cleaning * Remove debugging prints * First bids cases handled * Working on case functions * Cleaning before commit * Remove commented parts * proposition for case 3/1 * Add extension conversion for case3 * Cleaning prints * Improve case3 * Update prints * Changes as suggested * Changes as suggested 2 * Changes as suggested 3 * Regex on extensions * Changes according to suggestions * Changes according to suggestions 2 * Added unit tests * Change unit tests upon suggestions * Fix reorganize function
…ory if no subjects list is given (aramis-lab#1196) * Basic solution provided * Regex to find subjects * Create new method to return a subject list * Small fix * Change logic * Handle clinical data * Add unit tests * Changes upon suggestions * change API * Small Fix
…erly, enable converting to the same folder for fmap (aramis-lab#1198) * Adapt for mod_to_update and already renamed cases * Add sessions to conversion errors * Adapt unit tests * Suggestions + conversion_errors list updated * Add same logic for wrong suffixes * Change variable name * Add helper functions * Add unit test 1 * Modify helper functions and add unit tests * Small fixes
…ab#1199) * Add FMAP specificities to doc * Update conversion errors list * Modify doc * Small fix * Small fix 2
* refactor converters (unfinished) * some fixes * some more fixes * some more fixes 2 * some improvements * some improvements 2 * try fixing oasis issues * try fixing oasis issues again * fix adni to bids and simplify genfi to bids * work on API * make API more uniform * fix remaining bugs and continue uniformizing API * finish refactoring * fix call to find_image_path in adni_fmap * warn when n_procs or subjects options are not implemented * continue refactoring * fix bad merge * refine adni converter interface * post rebase fixes * fix bad rebase * fix errors introduced while rebasing * expose convert
…b#1206) * Preliminary todos * test create participants * Cleaning * Cleaning2 * Complete tests * Suggestions
* define the SUVRReferenceRegion enum * use it in CLI * use it in non regression tests * fix broken unit tests * other usages * update documentation * fix broken unit tests * do not break API * apply suggestion from code review
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.2.0 to 2.2.2. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](urllib3/urllib3@2.2.0...2.2.2) --- updated-dependencies: - dependency-name: urllib3 dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 1.4.0 to 1.5.0. - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](scikit-learn/scikit-learn@1.4.0...1.5.0) --- updated-dependencies: - dependency-name: scikit-learn dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…ling (aramis-lab#1215) * allow get_filename_no_ext to receive Path objects * change crop_nifti and add unit tests * use in pipelines and rework logic to download from server if necessary and mock in tests * fix bad mock * update checksum * fix checksum issue * fix syntax for python 3.9 and 3.10 * refactor a bit * factorize MNI template getting logic within a single function * update pydra pipelines a bit but not too much since not tested... * fix issue with nipype self contained
Bumps [certifi](https://github.com/certifi/python-certifi) from 2024.2.2 to 2024.7.4. - [Commits](certifi/python-certifi@2024.02.02...2024.07.04) --- updated-dependencies: - dependency-name: certifi dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…aramis-lab#1224) * move PETLinear pipeline to new pet module * update tests * remove unused crop_nifti_image
Bumps [zipp](https://github.com/jaraco/zipp) from 3.17.0 to 3.19.1. - [Release notes](https://github.com/jaraco/zipp/releases) - [Changelog](https://github.com/jaraco/zipp/blob/main/NEWS.rst) - [Commits](jaraco/zipp@v3.17.0...v3.19.1) --- updated-dependencies: - dependency-name: zipp dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…ramis-lab#1220) * Proposition for study_to_bids_id * Factoring * add test * Add to converters * Rename function * Apply to all datasets * Add nifd * Add ADNI * Changes upon suggestions * Use for adni-json * Add other uses * todo * changes upon suggestion
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Same PR #1227