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Merged
Remi-Gau merged 4 commits into from
Jun 28, 2021
Merged

add test to workflows #384

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815249e
add dummy data MoAE
Remi-Gau Jun 28, 2021
d479b59
fix moae demo
Remi-Gau Jun 28, 2021
96d91e8
add tests for smoothing and FFX model specification
Remi-Gau Jun 28, 2021
e6d2102
add gitignore
Remi-Gau Jun 28, 2021
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26 changes: 15 additions & 11 deletions demos/MoAE/moae_create_roi_extract_data.m
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Expand Up @@ -16,6 +16,7 @@

opt = moae_get_option();

opt.dir.roi = fullfile(opt.dir.derivatives, 'cpp_spm-roi');
opt.pipeline.type = 'stats';
opt = checkOptions(opt);

Expand All @@ -38,15 +39,18 @@
'mask1', maskImage, ...
'mask2', sphere);

[~, roiFile] = createRoi('expand', specification, conImage, pwd, saveROI);
output_dir = fullfile(opt.dir.roi, ['sub-' subLabel], 'roi');
spm_mkdir(output_dir);

[~, roiFile] = createRoi('expand', specification, conImage, output_dir, saveROI);

% rename mask image
newname.desc = 'right auditory cortex';
newname.task = '';
newname.label = '';
newname.p = '';
newname.k = '';
newname.MC = '';
newname.entities.desc = 'right auditory cortex';
newname.entities.task = '';
newname.entities.label = '';
newname.entities.p = '';
newname.entities.k = '';
newname.entities.MC = '';
rightRoiFile = renameFile(roiFile, newname);

%% same but with left hemisphere
Expand All @@ -56,10 +60,10 @@
'mask1', maskImage, ...
'mask2', sphere);

[~, roiFile] = createRoi('expand', specification, conImage, pwd, saveROI);
newname.desc = 'left auditory cortex';
[~, roiFile] = createRoi('expand', specification, conImage, output_dir, saveROI);
newname.entities.desc = 'left auditory cortex';
leftRoiFile = renameFile(roiFile, newname);

%%
right_data = spm_summarise(conImage, rightRoiFile);
left_data = spm_summarise(conImage, leftRoiFile);
right_data = spm_summarise(conImage, fullfile(output_dir, rightRoiFile));
left_data = spm_summarise(conImage, fullfile(output_dir, leftRoiFile));
1 change: 1 addition & 0 deletions demos/MoAE/moae_get_option.m
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Expand Up @@ -9,6 +9,7 @@

% task to analyze
opt.taskName = 'auditory';
opt.verbosity = 0;

% The directory where the data are located
opt.dir.raw = fullfile(fileparts(mfilename('fullpath')), 'inputs', 'raw');
Expand Down
4 changes: 2 additions & 2 deletions demos/MoAE/moae_slice_display.m
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Expand Up @@ -39,11 +39,11 @@

%% Layer 3 and 4: Contour of ROI

layers(3).color.file = rightRoiFile;
layers(3).color.file = fullfile(opt.dir.roi, ['sub-' subLabel], 'roi', rightRoiFile);
layers(3).color.map = [0 0 0];
layers(3).color.line_width = 2;

layers(4).color.file = leftRoiFile;
layers(4).color.file = fullfile(opt.dir.roi, ['sub-' subLabel], 'roi', leftRoiFile);
layers(4).color.map = [1 1 1];
layers(4).color.line_width = 2;

Expand Down
2 changes: 1 addition & 1 deletion src/batches/setBatchSubjectLevelGLMSpec.m
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Expand Up @@ -31,7 +31,7 @@
% correction is the one we center our model on
sliceOrder = getSliceOrder(opt);

if isempty(sliceOrder)
if isempty(sliceOrder) && ~opt.dryRun
% no slice order defined here so we fall back on using the number of
% slice in the first bold image to set the number of time bins
% we will use to upsample our model during regression creation
Expand Down
2 changes: 1 addition & 1 deletion src/defaults/checkOptions.m
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Expand Up @@ -121,7 +121,7 @@
fieldsToSet.subjects = {[]};
fieldsToSet.zeropad = 2;

fieldsToSet.query.modality = {'anat', 'func', 'dwi'};
fieldsToSet.query.modality = {'anat', 'func'};

fieldsToSet.anatReference.type = 'T1w';
fieldsToSet.anatReference.session = '';
Expand Down
1 change: 1 addition & 0 deletions tests/dummyData/MoAE/.gitignore
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@@ -0,0 +1 @@
derivatives/**
33 changes: 33 additions & 0 deletions tests/dummyData/MoAE/derivatives/cpp_spm-preproc/dataset_description.json
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@@ -0,0 +1,33 @@
{
"Name": "",
"BIDSVersion": "",
"DatasetType": "derivative",
"License": "",
"Authors": "",
"Acknowledgements": "",
"HowToAcknowledge": "",
"Funding": "",
"ReferencesAndLinks": "",
"DatasetDOI": "",
"HEDVersion": "",
"GeneratedBy": [
{
"Name": "cpp_spm-preproc",
"Version": "",
"Description": "",
"CodeURL": "",
"Container": {
"Type": "",
"Tag": ""
}
},
{
"Name": "cpp_spm-preproc"
}
],
"SourceDatasets": {
"DOI": "",
"URL": "",
"Version": ""
}
}
236 changes: 236 additions & 0 deletions ...preproc/jobs/auditory/sub-01/20210628_0713_jobs_matlabbatch_SPM12_segment_skullstrip.json
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@@ -0,0 +1,236 @@
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Empty file added ...-preproc/jobs/auditory/sub-01/20210628_0713_jobs_matlabbatch_SPM12_segment_skullstrip.mat
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