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[FIX] update initialization matlabbatch #397

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Merged
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Aug 18, 2021
Merged

[FIX] update initialization matlabbatch #397

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8a0eef4
update initialization matlabbatch
Remi-Gau Aug 17, 2021
3eecaa2
[FIX] update default data type value related to image calculation batch
Remi-Gau Aug 17, 2021
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2 changes: 1 addition & 1 deletion manualTests/test_setBatchCoregistrationFmap.m
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Expand Up @@ -19,7 +19,7 @@ function test_setBatchCoregistrationFmapBasic()

[~, opt, BIDS] = getData(opt);

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchCoregistrationFmap(matlabbatch, BIDS, opt, subID);

directory = fullfile(opt.derivativesDir, ...
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2 changes: 1 addition & 1 deletion manualTests/test_setBatchCreateVDMs.m
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Expand Up @@ -20,7 +20,7 @@ function test_setBatchCreateVDMsBasic()

[~, opt, BIDS] = getData(opt);

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchCreateVDMs(matlabbatch, BIDS, opt, subID);

% matlabbatch{1}.spm.tools.fieldmap.calculatevdm.subj
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2 changes: 1 addition & 1 deletion src/templates/bidsTemplateWorkflow.m
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Expand Up @@ -11,7 +11,7 @@ function bidsTemplateWorkflow(opt)

printProcessingSubject(iSub, subLabel);

matlabbatch = [];
matlabbatch = {};

matlabbatch = setBatchSomeBatch(matlabbatch, BIDS, opt, subLabel);

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2 changes: 1 addition & 1 deletion src/workflows/bidsConcatBetaTmaps.m
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Expand Up @@ -93,7 +93,7 @@ function bidsConcatBetaTmaps(opt, funcFWHM, deleteIndBeta, deleteIndTmaps)
% beta maps
outputName = ['4D_beta_', num2str(funcFWHM), '.nii'];

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatch3Dto4D(matlabbatch, beta_maps, RT, outputName);

% t-maps
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4 changes: 2 additions & 2 deletions src/workflows/bidsCreateVDM.m
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Expand Up @@ -40,11 +40,11 @@ function bidsCreateVDM(opt)
[fileName, subFuncDataDir] = getBoldFilename(BIDS, subLabel, sessions{1}, runs{1}, opt);
spmup_basics(fullfile(subFuncDataDir, fileName), 'mean');

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchCoregistrationFmap(matlabbatch, BIDS, opt, subLabel);
saveAndRunWorkflow(matlabbatch, 'coregister_fmap', opt, subLabel);

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchCreateVDMs(matlabbatch, BIDS, opt, subLabel);
saveAndRunWorkflow(matlabbatch, 'create_vdm', opt, subLabel);

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2 changes: 1 addition & 1 deletion src/workflows/bidsFFX.m
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Expand Up @@ -49,7 +49,7 @@ function bidsFFX(action, opt, funcFWHM)

printProcessingSubject(iSub, subLabel);

matlabbatch = [];
matlabbatch = {};

switch action

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2 changes: 1 addition & 1 deletion src/workflows/bidsLesionAbnormalitiesDetection.m
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Expand Up @@ -50,7 +50,7 @@ function bidsLesionAbnormalitiesDetection(opt)
end
end

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchLesionAbnormalitiesDetection(matlabbatch, opt, images);

saveAndRunWorkflow(matlabbatch, 'LesionAbnormalitiesDetection', opt, subLabel);
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2 changes: 1 addition & 1 deletion src/workflows/bidsLesionOverlapMap.m
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Expand Up @@ -24,7 +24,7 @@ function bidsLesionOverlapMap(opt)

printProcessingSubject(iSub, subLabel);

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchLesionOverlapMap(matlabbatch, BIDS, opt, subLabel);

saveAndRunWorkflow(matlabbatch, 'LesionOverlapMap', opt, subLabel);
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2 changes: 1 addition & 1 deletion src/workflows/bidsLesionSegmentation.m
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Expand Up @@ -22,7 +22,7 @@ function bidsLesionSegmentation(opt)

printProcessingSubject(iSub, subLabel);

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchLesionSegmentation(matlabbatch, BIDS, opt, subLabel);

saveAndRunWorkflow(matlabbatch, 'LesionSegmentation', opt, subLabel);
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8 changes: 4 additions & 4 deletions src/workflows/bidsRFX.m
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Expand Up @@ -46,7 +46,7 @@ function bidsRFX(action, opt, funcFWHM, conFWHM)

case 'smoothContrasts'

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchSmoothConImages(matlabbatch, opt, funcFWHM, conFWHM);

saveAndRunWorkflow(matlabbatch, ...
Expand All @@ -65,7 +65,7 @@ function bidsRFX(action, opt, funcFWHM, conFWHM)
% - needs to be improved (maybe??) as the structural and mask may vary for
% different analysis
% ------
matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchMeanAnatAndMask(matlabbatch, ...
opt, ...
funcFWHM, ...
Expand All @@ -74,7 +74,7 @@ function bidsRFX(action, opt, funcFWHM, conFWHM)

% TODO
% saving needs to be improved (maybe??) as the name may vary with FXHM and contrast
matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchFactorialDesign(matlabbatch, opt, funcFWHM, conFWHM);

% Load the list of contrasts of interest for the RFX
Expand All @@ -86,7 +86,7 @@ function bidsRFX(action, opt, funcFWHM, conFWHM)
% TODO
% saving needs to be improved (maybe??) as the name may vary with FXHM and contrast
rfxDir = getRFXdir(opt, funcFWHM, conFWHM);
matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchGroupLevelContrasts(matlabbatch, grpLvlCon, rfxDir);
saveAndRunWorkflow(matlabbatch, 'contrasts_rfx', opt);

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2 changes: 1 addition & 1 deletion src/workflows/bidsRealignReslice.m
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Expand Up @@ -22,7 +22,7 @@ function bidsRealignReslice(opt)

printProcessingSubject(iSub, subLabel);

matlabbatch = [];
matlabbatch = {};
[matlabbatch, ~] = setBatchRealign( ...
matlabbatch, ...
BIDS, ...
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2 changes: 1 addition & 1 deletion src/workflows/bidsRealignUnwarp.m
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Expand Up @@ -25,7 +25,7 @@ function bidsRealignUnwarp(opt)

printProcessingSubject(iSub, subLabel);

matlabbatch = [];
matlabbatch = {};
[matlabbatch, ~] = setBatchRealign( ...
matlabbatch, ...
BIDS, ...
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4 changes: 2 additions & 2 deletions src/workflows/bidsResliceTpmToFunc.m
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Expand Up @@ -34,7 +34,7 @@ function bidsResliceTpmToFunc(opt)
[anatImage, anatDataDir] = getAnatFilename(BIDS, subLabel, opt);
TPMs = validationInputFile(anatDataDir, anatImage, 'c[123]');

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchReslice(matlabbatch, ...
fullfile(meanFuncDir, meanImage), ...
cellstr(TPMs));
Expand All @@ -54,7 +54,7 @@ function bidsResliceTpmToFunc(opt)

expression = sprintf('(i1+i2+i3)>%f', opt.skullstrip.threshold);

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchImageCalculation(matlabbatch, input, output, meanFuncDir, expression);

saveAndRunWorkflow(matlabbatch, 'create_functional_brain_mask', opt, subLabel);
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6 changes: 3 additions & 3 deletions src/workflows/bidsResults.m
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Expand Up @@ -47,15 +47,15 @@ function bidsResults(opt, funcFWHM, conFWHM)
case 'run'
warning('run level not implemented yet');

% matlabbatch = [];
% matlabbatch = {};
% saveMatlabBatch(matlabbatch, 'computeFfxResults', opt, subID);

case 'subject'

% For each subject
for iSub = 1:numel(opt.subjects)

matlabbatch = [];
matlabbatch = {};

subLabel = opt.subjects{iSub};

Expand Down Expand Up @@ -86,7 +86,7 @@ function bidsResults(opt, funcFWHM, conFWHM)

case 'dataset'

matlabbatch = [];
matlabbatch = {};

results.dir = getRFXdir(opt, funcFWHM, conFWHM);
results.contrastNb = 1;
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2 changes: 1 addition & 1 deletion src/workflows/bidsRoiBasedGLM.m
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Expand Up @@ -32,7 +32,7 @@ function bidsRoiBasedGLM(opt)

printProcessingSubject(iSub, subLabel);

matlabbatch = [];
matlabbatch = {};

matlabbatch = setBatchSubjectLevelGLMSpec(matlabbatch, BIDS, opt, subLabel, funcFWHM);

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2 changes: 1 addition & 1 deletion src/workflows/bidsSTC.m
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Expand Up @@ -37,7 +37,7 @@ function bidsSTC(opt)

printProcessingSubject(iSub, subLabel);

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchSTC(matlabbatch, BIDS, opt, subLabel);

saveAndRunWorkflow(matlabbatch, 'STC', opt, subLabel);
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2 changes: 1 addition & 1 deletion src/workflows/bidsSegmentSkullStrip.m
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Expand Up @@ -23,7 +23,7 @@ function bidsSegmentSkullStrip(opt)

printProcessingSubject(iSub, subLabel);

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchSelectAnat(matlabbatch, BIDS, opt, subLabel);

% dependency from file selector ('Anatomical')
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2 changes: 1 addition & 1 deletion src/workflows/bidsSmoothing.m
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Expand Up @@ -24,7 +24,7 @@ function bidsSmoothing(funcFWHM, opt)

printProcessingSubject(iSub, subLabel);

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchSmoothingFunc(matlabbatch, BIDS, opt, subLabel, funcFWHM);

saveAndRunWorkflow(matlabbatch, ['smoothing_FWHM-' num2str(funcFWHM)], opt, subLabel);
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2 changes: 1 addition & 1 deletion src/workflows/bidsSpatialPrepro.m
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Expand Up @@ -49,7 +49,7 @@ function bidsSpatialPrepro(opt)

parfor iSub = 1:numel(opt.subjects)

matlabbatch = [];
matlabbatch = {};

subLabel = opt.subjects{iSub};

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2 changes: 1 addition & 1 deletion src/workflows/bidsWholeBrainFuncMask.m
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Expand Up @@ -28,7 +28,7 @@
opt.orderBatches.skullStripping = 2;

% make matlab batch for segment and skullstip
matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchSegmentation(matlabbatch, opt, meanFuncFileName);

matlabbatch = setBatchSkullStripping(matlabbatch, BIDS, opt, subLabel);
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2 changes: 1 addition & 1 deletion tests/test_setBatch3Dto4D.m
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Expand Up @@ -16,7 +16,7 @@ function test_setBatch3Dto4DBasic()

RT = 2;

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatch3Dto4D(matlabbatch, volumesList, RT);

expectedBatch{1}.spm.util.cat.vols = volumesList;
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2 changes: 1 addition & 1 deletion tests/test_setBatchComputeVDM.m
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Expand Up @@ -13,7 +13,7 @@ function test_setBatchComputeVDMBasic()
fmapType = 'phasediff';
refImage = fullfile(pwd, 'mean_sub-01-task-rest_bold.nii');

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchComputeVDM(matlabbatch, fmapType, refImage);

expectedBatch = returnExpectedBatch(refImage);
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2 changes: 1 addition & 1 deletion tests/test_setBatchFactorialDesign.m
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Expand Up @@ -16,7 +16,7 @@ function test_setBatchFactorialDesignBasic()
opt = setOptions('vismotion');
opt.subjects = {'01' '02'};

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchFactorialDesign(matlabbatch, opt, funcFWHM, conFWHM);

% TODO
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4 changes: 2 additions & 2 deletions tests/test_setBatchMeanAnatAndMask.m
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Expand Up @@ -33,7 +33,7 @@ function test_setBatchMeanAnatAndMaskBasic()
imcalc.output = 'meanAnat.nii';
imcalc.outdir{1} = pwd;
imcalc.expression = '(i1+i2)/2';
imcalc.options.dtype = 4;
imcalc.options.dtype = 16;

expectedBatch{1}.spm.util.imcalc = imcalc;

Expand All @@ -51,7 +51,7 @@ function test_setBatchMeanAnatAndMaskBasic()
imcalc.output = 'meanMask.nii';
imcalc.outdir{1} = pwd;
imcalc.expression = '(i1+i2)>0.75*2';
imcalc.options.dtype = 4;
imcalc.options.dtype = 16;

expectedBatch{2}.spm.util.imcalc = imcalc;

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2 changes: 1 addition & 1 deletion tests/test_setBatchRealign.m
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Expand Up @@ -21,7 +21,7 @@ function test_setBatchRealignBasic()
opt = setOptions('MoAE', subLabel);
[BIDS, opt] = getData(opt);

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchRealign(matlabbatch, BIDS, opt, subLabel);

expectedBatch{1}.spm.spatial.realignunwarp.eoptions.weight = {''};
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6 changes: 3 additions & 3 deletions tests/test_setBatchResults.m
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Expand Up @@ -23,7 +23,7 @@ function test_setBatchResultsBasic()
result.Contrasts.p = 0.05;
result.Contrasts.k = 0;

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchResults(matlabbatch, result);

expectedBatch = returnBasicExpectedResultsBatch();
Expand Down Expand Up @@ -74,7 +74,7 @@ function test_setBatchResultsExport()
result.Output = opt.result.Steps(iStep).Output;
result.space = opt.space;

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchResults(matlabbatch, result);

expectedBatch = returnBasicExpectedResultsBatch();
Expand Down Expand Up @@ -124,7 +124,7 @@ function test_setBatchResultsMontage()
result.Output = opt.result.Steps(iStep).Output;
result.space = opt.space;

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchResults(matlabbatch, result);

expectedBatch = returnBasicExpectedResultsBatch();
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6 changes: 3 additions & 3 deletions tests/test_setBatchSegmentation.m
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Expand Up @@ -17,7 +17,7 @@ function test_setBatchSegmentationPipeline()

opt.orderBatches.selectAnat = 1;

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchSegmentation(matlabbatch, opt);

expectedBatch = returnExpectedBatch(spmLocation);
Expand All @@ -43,15 +43,15 @@ function test_setBatchSegmentationImages()
anatImage = returnLocalAnatFilename();

% check with one file
matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchSegmentation(matlabbatch, opt, anatImage);
expectedBatch = returnExpectedBatch(spmLocation);
expectedBatch{end}.spm.spatial.preproc.channel.vols{1} = anatImage;

assertEqual(expectedBatch, matlabbatch);

% check with several files passed as a cell
matlabbatch = [];
matlabbatch = {};
anatImage = {anatImage; anatImage};
matlabbatch = setBatchSegmentation(matlabbatch, opt, anatImage);
expectedBatch{end}.spm.spatial.preproc.channel.vols = anatImage;
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2 changes: 1 addition & 1 deletion tests/test_setBatchSelectAnat.m
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Expand Up @@ -20,7 +20,7 @@ function test_setBatchSelectAnatBasic()

[BIDS, opt] = getData(opt);

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchSelectAnat(matlabbatch, BIDS, opt, subLabel);

expectedBatch{1}.cfg_basicio.cfg_named_file.name = 'Anatomical';
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2 changes: 1 addition & 1 deletion tests/test_setBatchSkullStripping.m
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Expand Up @@ -77,7 +77,7 @@ function test_setBatchSkullStrippingBasic()
imcalc.output = ['m' strrep(expectedFileName, '.nii', '_skullstripped.nii')];
imcalc.outdir = {expectedAnatDataDir};
imcalc.expression = sprintf('i1.*((i2+i3+i4)>%f)', opt.skullstrip.threshold);
imcalc.options.dtype = 4;
imcalc.options.dtype = 16;

expected_batch = {};
expected_batch{end + 1}.spm.util.imcalc = imcalc;
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2 changes: 1 addition & 1 deletion tests/test_setBatchSmoothConImages.m
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Expand Up @@ -18,7 +18,7 @@ function test_setBatchSmoothConImagesBasic()

[~, opt] = getData(opt);

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchSmoothConImages(matlabbatch, opt, funcFWHM, conFWHM);

expectedBatch{1}.spm.spatial.smooth.fwhm = [6 6 6];
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2 changes: 1 addition & 1 deletion tests/test_setBatchSmoothing.m
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Expand Up @@ -15,7 +15,7 @@ function test_setBatchSmoothingBasic()

images = { fullfile(pwd, 'sub-01_T1w.nii') };

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchSmoothing(matlabbatch, images, FWHM, prefix);

expectedBatch{1}.spm.spatial.smooth.fwhm = [6 6 6];
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2 changes: 1 addition & 1 deletion tests/test_setBatchSmoothingFunc.m
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Expand Up @@ -34,7 +34,7 @@ function test_setBatchSmoothingFuncBasic()
filename ext]);
system(sprintf('touch %s', fileName));

matlabbatch = [];
matlabbatch = {};
matlabbatch = setBatchSmoothingFunc(matlabbatch, BIDS, opt, subLabel, funcFWHM);

expectedBatch{1}.spm.spatial.smooth.fwhm = [6 6 6];
Expand Down
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