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[FIX] Remove goodness of fit for dataset level and update container definitions #1265

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merged 8 commits into from
Jul 8, 2024
Merged

[FIX] Remove goodness of fit for dataset level and update container definitions #1265

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cf0ce16
misc fix
Remi-Gau Jul 7, 2024
b708318
rm GoF for dataset level
Remi-Gau Jul 7, 2024
800bcc7
Merge remote-tracking branch 'upstream/main' into fix/1237
Remi-Gau Jul 7, 2024
c20c135
install java
Remi-Gau Jul 7, 2024
f881d24
add zip
Remi-Gau Jul 8, 2024
2bcfef4
update changelog
Remi-Gau Jul 8, 2024
01ab62a
add unzip
Remi-Gau Jul 8, 2024
bd7359b
fix tests
Remi-Gau Jul 8, 2024
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1 change: 1 addition & 0 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -202,6 +202,7 @@ jobs:
--space MNI152NLin2009cAsym \
--skip_validation \
--fwhm 0 \
--participant_label 01 02 \
--verbosity 3 \
--options /options/ds000001.json

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2 changes: 1 addition & 1 deletion demos/openneuro/Makefile
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Expand Up @@ -23,7 +23,7 @@ data_ds000001:
cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/func/*json -J 12
cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/anat/*MNI*desc-preproc*.nii.gz -J 12
cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/func/*MNI*desc-preproc*.nii.gz -J 12
cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/func/*MNI*desc-*bold.nii.gz -J 12
cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/func/*MNI*desc-*bold.nii.gz -J 12

data_ds000114:
mkdir -p inputs
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1 change: 0 additions & 1 deletion src/batches/stats/setBatchEstimateModel.m
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Expand Up @@ -91,7 +91,6 @@

matlabbatch = returnEstimateModelBatch(matlabbatch, spmMatFile, opt);
opt.orderBatches.estimate = numel(matlabbatch);
matlabbatch = setBatchGoodnessOfFit(matlabbatch, opt);
matlabbatch = setBatchInformationCriteria(matlabbatch, opt, rfxDir);

matlabbatch{end + 1}.spm.stats.review.spmmat = spmMatFile; %#ok<*AGROW>
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14 changes: 6 additions & 8 deletions tests/tests_slow/tests_workflows/stats/test_bidsRFX.m
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Expand Up @@ -19,7 +19,7 @@ function test_bidsRFX_rfx()
% 2 dummy contrasts
% 2 contrasts
nbGroupLevelModels = 4;
nbBatchPerModel = 8;
nbBatchPerModel = 7;
if bids.internal.is_octave()
nbBatchPerModel = 5;
end
Expand All @@ -35,7 +35,7 @@ function test_bidsRFX_rfx()

% setBatchEstimateModel creates 3 batches for each model (estimate, review, figure)
batchOrder = extendBatchOrder();
idx = 9:6:(nbGroupLevelModels * nbBatchPerModel);
idx = 9:5:(nbGroupLevelModels * nbBatchPerModel);
if bids.internal.is_octave()
idx = 9:3:(nbGroupLevelModels * nbBatchPerModel);
end
Expand All @@ -57,7 +57,7 @@ function test_bidsRFX_no_overwrite_smoke_test()

matlabbatch = bidsRFX('RFX', opt);

expectedNbBatch = 8;
expectedNbBatch = 7;
if bids.internal.is_octave()
expectedNbBatch = 5;
end
Expand All @@ -80,14 +80,13 @@ function test_bidsRFX_within_group_ttest()
if bids.internal.is_octave()
assertEqual(numel(matlabbatch), 10);
else
assertEqual(numel(matlabbatch), 16);
assertEqual(numel(matlabbatch), 14);
end

% creates 1 batch for
% - specify
% - figure
% - estimate
% - MACS: goodness of fit
% - MACS: model space
% - MACS: information criteria
% - review
Expand All @@ -110,7 +109,7 @@ function test_bidsRFX_within_group_ttest()
fileparts(matlabbatch{8}.spm.stats.fmri_est.spmmat{1}));
else
assertEqual(matlabbatch{3}.spm.stats.factorial_design.dir{1}, ...
fileparts(matlabbatch{11}.spm.stats.fmri_est.spmmat{1}));
fileparts(matlabbatch{10}.spm.stats.fmri_est.spmmat{1}));
end

end
Expand Down Expand Up @@ -191,7 +190,7 @@ function test_bidsRFX_several_datasets_level()
assertEqual(summary, batchOrder);

nbGroupLevelModelsReturned = 1;
nbBatchPerModel = 8;
nbBatchPerModel = 7;
if bids.internal.is_octave()
nbBatchPerModel = 5;
end
Expand Down Expand Up @@ -250,7 +249,6 @@ function test_bidsRFX_contrast()
batchOrder = {};
end
extension = {'stats', 'fmri_est'; ...
'tools', 'MACS'; ... % skip on octave
'tools', 'MACS'; ...
'tools', 'MACS'; ...
'stats', 'review'; ...
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