Merge pull request #418 from Remi-Gau/bug-fix

[FIX] remove extra submodules and properly compute run level contrasts
cpp-lln-lab · Oct 1, 2021 · f58b6f1 · f58b6f1
2 parents 7750416 + 816f73d
commit f58b6f1
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Showing 49 changed files with 430 additions and 212 deletions.
diff --git a/.github/workflows/run_system_tests.yml b/.github/workflows/run_system_tests.yml
@@ -17,14 +17,12 @@ name: system tests
 on:
   push:
     branches:
-      - master
       - main
   pull_request:
     branches: 
-      - 'master'
       - 'main'
   schedule:
-    - cron: "* * 1 * *"
+    - cron: "0 0 1 * *"
 
 env:
   OCTFLAGS: --no-gui --no-window-system --silent

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -21,7 +21,7 @@ on:
   pull_request:
     branches: '*'
   schedule:
-    - cron: "* * 1 * *"
+    - cron: "0 0 1 * *"
 
 env:
   OCTFLAGS: --no-gui --no-window-system --silent

diff --git a/.gitmodules b/.gitmodules
@@ -12,4 +12,4 @@
 	url = https://github.com/bramzandbelt/slice_display.git
 [submodule "lib/brain_colours"]
 	path = lib/brain_colours
-	url = https://github.com/CPernet/brain_colours.git
+	url = https://github.com/CPernet/brain_colours.git
diff --git a/demos/MoAE/moae_create_roi_extract_data.m b/demos/MoAE/moae_create_roi_extract_data.m
@@ -23,7 +23,7 @@
 % we get the con image to extract data
 % we can do this by using the "label-XXXX" from the mask
 p = bids.internal.parse_filename(spm_file(maskImage, 'filename'));
-conImage = spm_select('FPList', ffxDir, ['^con_' p.label '.nii$']);
+conImage = spm_select('FPList', ffxDir, ['^con_' p.entities.label '.nii$']);
 
 %% Create ROI right auditory cortex
 sphere.location = [57 -22 11];
@@ -35,12 +35,12 @@
 [~, roiFile] = createRoi('expand', specification, conImage, pwd, 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

diff --git a/demos/MoAE/moae_run.m b/demos/MoAE/moae_run.m
@@ -23,7 +23,7 @@
 download_moae_ds(downloadData);
 
 %% Run batches
-reportBIDS(opt);
+% reportBIDS(opt);
 bidsCopyRawFolder(opt, 1);
 
 % In case you just want to run segmentation and skull stripping

diff --git a/demos/MoAE/moae_slice_display.m b/demos/MoAE/moae_slice_display.m
@@ -31,7 +31,7 @@
 %
 %   - t-statistics opacity-coded
 
-spmTImage = spm_select('FPList', ffxDir, ['^spmT_' p.label '.nii$']);
+spmTImage = spm_select('FPList', ffxDir, ['^spmT_' p.entities.label '.nii$']);
 layers(2).opacity.file = spmTImage;
 
 layers(2).opacity.range = [2 3];

diff --git a/lib/CPP_ROI b/lib/CPP_ROI
diff --git a/lib/bids-matlab b/lib/bids-matlab
diff --git a/manualTests/test_moae.m b/manualTests/test_moae.m
@@ -47,7 +47,7 @@
 
   %% Run batches
 
-  reportBIDS(opt);
+  % reportBIDS(opt);
 
   bidsCopyRawFolder(opt, 1);
 

diff --git a/src/batches/setBatchEstimateModel.m b/src/batches/setBatchEstimateModel.m
@@ -59,7 +59,7 @@
   matlabbatch{end}.spm.stats.fmri_est.spmmat = spmMatFile;
 
   writeResiduals = true();
-  if ~opt.glm.QA.do
+  if ~opt.QA.glm.do
     writeResiduals = false();
   end
   matlabbatch{end}.spm.stats.fmri_est.write_residuals = writeResiduals;

diff --git a/src/batches/setBatchResults.m b/src/batches/setBatchResults.m
@@ -21,11 +21,12 @@
   %
   % (C) Copyright 2019 CPP_SPM developers
 
-  result.outputNameStructure.sub = result.label;
-  result.outputNameStructure.desc = result.Contrasts.Name;
-  result.outputNameStructure.p = num2str(result.Contrasts.p);
-  result.outputNameStructure.k = num2str(result.Contrasts.k);
-  result.outputNameStructure.MC = result.Contrasts.MC;
+  result.outputNameStructure.use_schema = false;
+  result.outputNameStructure.entities.sub = result.label;
+  result.outputNameStructure.entities.desc = result.Contrasts.Name;
+  result.outputNameStructure.entities.p = num2str(result.Contrasts.p);
+  result.outputNameStructure.entities.k = num2str(result.Contrasts.k);
+  result.outputNameStructure.entities.MC = result.Contrasts.MC;
 
   fieldsToSet = returnDefaultResultsStructure();
   result = setFields(result, fieldsToSet);
@@ -58,13 +59,13 @@
 
   if result.Output.thresh_spm
     result.outputNameStructure.ext = '';
-    export{end + 1}.tspm.basename = createFilename(result.outputNameStructure);
+    export{end + 1}.tspm.basename = bids.create_filename(result.outputNameStructure);
   end
 
   if result.Output.binary
     result.outputNameStructure.ext = '';
-    result.outputNameStructure.type = 'mask';
-    export{end + 1}.binary.basename = createFilename(result.outputNameStructure);
+    result.outputNameStructure.suffix = 'mask';
+    export{end + 1}.binary.basename = bids.create_filename(result.outputNameStructure);
   end
 
   if result.Output.NIDM_results
@@ -92,8 +93,8 @@
 
     % Not sure why the name of the figure does not come out right
     result.outputNameStructure.ext = '';
-    result.outputNameStructure.type = 'montage';
-    matlabbatch{end + 1}.spm.util.print.fname = createFilename(result.outputNameStructure);
+    result.outputNameStructure.suffix = 'montage';
+    matlabbatch{end + 1}.spm.util.print.fname = bids.create_filename(result.outputNameStructure);
     matlabbatch{end}.spm.util.print.fig.figname = 'SliceOverlay';
     matlabbatch{end}.spm.util.print.opts = 'png';
 

diff --git a/src/batches/setBatchSubjectLevelContrasts.m b/src/batches/setBatchSubjectLevelContrasts.m
@@ -25,8 +25,12 @@
 
   spmMatFile = cellstr(fullfile(ffxDir, 'SPM.mat'));
 
+  load(spmMatFile{1}, 'SPM');
+
+  model = spm_jsonread(opt.model.file);
+
   % Create Contrasts
-  contrasts = specifyContrasts(ffxDir, opt.taskName, opt);
+  contrasts = specifyContrasts(SPM, opt.taskName, model);
   for icon = 1:size(contrasts, 2)
     consess{icon}.tcon.name = contrasts(icon).name; %#ok<*AGROW>
     consess{icon}.tcon.convec = contrasts(icon).C;

diff --git a/src/batches/setBatchSubjectLevelGLMSpec.m b/src/batches/setBatchSubjectLevelGLMSpec.m
@@ -37,7 +37,7 @@
     % we will use to upsample our model during regression creation
     fileName = bids.query(BIDS, 'data', ...
                           'sub', subLabel, ...
-                          'type', 'bold');
+                          'suffix', 'bold');
     fileName = strrep(fileName{1}, '.gz', '');
     hdr = spm_vol(fileName);
     % we are assuming axial acquisition here

diff --git a/src/batches/setBatchSubjectLevelResults.m b/src/batches/setBatchSubjectLevelResults.m
@@ -39,16 +39,18 @@
   result.contrastNb = getContrastNb(result);
 
   result.outputNameStructure = struct( ...
-                                      'type', 'spmT', ...
+                                      'suffix', 'spmT', ...
                                       'ext', '.nii', ...
-                                      'sub', '', ...
-                                      'task', opt.taskName, ...
-                                      'space', opt.space, ...
-                                      'desc', '', ...
-                                      'label', 'XXXX', ...
-                                      'p', '', ...
-                                      'k', '', ...
-                                      'MC', '');
+                                      'use_schema', 'false', ...
+                                      'entities', struct('sub', '', ...
+                                                         'task', opt.taskName, ...
+                                                         'space', opt.space, ...
+                                                         'desc', '', ...
+                                                         'label', sprintf('%04.0f', ...
+                                                                          result.contrastNb), ...
+                                                         'p', '', ...
+                                                         'k', '', ...
+                                                         'MC', ''));
 
   matlabbatch = setBatchResults(matlabbatch, result);
 

diff --git a/src/defaults/createDefaultModel.m b/src/defaults/createDefaultModel.m
@@ -78,7 +78,7 @@
   % list all the *events.tsv files for that task and make a lis of all the
   % trial_types
   eventFiles = bids.query(BIDS, 'data', ...
-                          'type', 'events', ...
+                          'suffix', 'events', ...
                           'task', opt.taskName);
 
   trialTypeList = {};

diff --git a/src/fieldmaps/getMetadataFromIntendedForFunc.m b/src/fieldmaps/getMetadataFromIntendedForFunc.m
@@ -44,7 +44,7 @@
 
     funcMetadata = bids.query(BIDS, 'metadata', ...
                               'modality', 'func', ...
-                              'type', fragments.type, ...
+                              'suffix', fragments.suffix, ...
                               'sub', fragments.sub, ...
                               'ses', fragments.ses, ...
                               'run', fragments.run, ...

diff --git a/src/fieldmaps/getVdmFile.m b/src/fieldmaps/getVdmFile.m
@@ -21,13 +21,15 @@
 
   fragments = bids.internal.parse_filename(boldFilename);
 
-  if ~isfield(fragments, 'ses')
-    fragments.ses = '';
+  entities = fragments.entities;
+
+  if ~isfield(entities, 'ses')
+    entities.ses = '';
   end
 
   modalities = bids.query(BIDS, 'modalities', ...
-                          'sub', fragments.sub, ...
-                          'ses', fragments.ses);
+                          'sub', entities.sub, ...
+                          'ses', entities.ses);
 
   if opt.useFieldmaps && any(ismember('fmap', modalities))
     % We loop through the field maps and find the one that is intended for this
@@ -37,13 +39,13 @@
 
     fmapFiles = bids.query(BIDS, 'data', ...
                            'modality', 'fmap', ...
-                           'sub', fragments.sub, ...
-                           'ses', fragments.ses);
+                           'sub', entities.sub, ...
+                           'ses', entities.ses);
 
     fmapMetadata = bids.query(BIDS, 'metadata', ...
                               'modality', 'fmap', ...
-                              'sub', fragments.sub, ...
-                              'ses', fragments.ses);
+                              'sub', entities.sub, ...
+                              'ses', entities.ses);
 
     for  iFile = 1:size(fmapFiles, 1)
 

diff --git a/src/getAnatFilename.m b/src/getAnatFilename.m
@@ -31,7 +31,7 @@
   anat = bids.query(BIDS, 'data', ...
                     'sub', subLabel, ...
                     'ses', anatSession, ...
-                    'type', anatSuffix);
+                    'suffix', anatSuffix);
 
   if isempty(anat)
 
@@ -58,7 +58,7 @@
 
 function checkAvailableSuffix(BIDS, subLabel, anatType)
 
-  availableSuffixes = bids.query(BIDS, 'types', ...
+  availableSuffixes = bids.query(BIDS, 'suffixes', ...
                                  'sub', subLabel);
 
   if ~strcmp(anatType, availableSuffixes)

diff --git a/src/getBoldFilename.m b/src/getBoldFilename.m
@@ -30,6 +30,12 @@
 
   [BIDS, subID, sessionID, runID, opt] = deal(varargin{:});
 
+  if isempty(opt.query)
+    opt.query = struct('extension', '.nii');
+  else
+    opt.query.extension = '.nii';
+  end
+
   % get the filename for this bold run for this task
   boldFileName = getInfo(BIDS, subID, opt, 'Filename', sessionID, runID, 'bold');
 

diff --git a/src/getData.m b/src/getData.m
@@ -1,4 +1,4 @@
-function [BIDS, opt] = getData(opt, BIDSdir, type)
+function [BIDS, opt] = getData(opt, BIDSdir, suffix)
   %
   % Reads the specified BIDS data set and updates the list of subjects to analyze.
   %
@@ -35,14 +35,14 @@
   end
   derivativesDir = BIDSdir;
 
-  if nargin < 3 || (exist('type', 'var') && isempty(type))
-    type = 'bold';
+  if nargin < 3 || (exist('type', 'var') && isempty(suffix))
+    suffix = 'bold';
   end
 
   if isfield(opt, 'taskName')
     fprintf(1, 'FOR TASK: %s\n', opt.taskName);
   else
-    type = 'T1w';
+    suffix = 'T1w';
   end
 
   % we let SPM figure out what is in this BIDS data set
@@ -66,29 +66,29 @@
   % get metadata for bold runs for that task
   % we take those from the first run of the first subject assuming it can
   % apply to all others.
-  opt = getMetaData(BIDS, opt, opt.subjects, type);
+  opt = getMetaData(BIDS, opt, opt.subjects, suffix);
 
   fprintf(1, 'WILL WORK ON SUBJECTS\n');
   disp(opt.subjects);
 
 end
 
-function opt = getMetaData(BIDS, opt, subjects, type)
+function opt = getMetaData(BIDS, opt, subjects, suffix)
 
   % TODO
   % THIS NEEDS FIXING AS WE MIGHT WANT THE METADATA OF THE SUBJECTS SELECTED
   % RATHER THAN THE FIRST SUBJECT OF THE DATASET
 
-  switch type
+  switch suffix
     case 'bold'
       metadata = bids.query(BIDS, 'metadata', ...
                             'task', opt.taskName, ...
                             'sub', subjects{1}, ...
-                            'type', type);
+                            'suffix', suffix);
     case 'T1w'
       metadata = bids.query(BIDS, 'metadata', ...
                             'sub', subjects{1}, ...
-                            'type', type);
+                            'suffix', suffix);
   end
 
   if iscell(metadata)

diff --git a/src/getInfo.m b/src/getInfo.m
@@ -19,7 +19,7 @@
   % If info = ``filename``, this returns the name of the file for a specified
   % session and run::
   %
-  %   filenames = getInfo(BIDS, subLabel, opt, 'filename', sessionID, runID, type)
+  %   filenames = getInfo(BIDS, subLabel, opt, 'filename', sessionID, runID, suffix)
   %
   %
   % :param BIDS:            returned by bids.layout when exploring a BIDS data set.
@@ -42,8 +42,8 @@
   % :param runIdx:          run index label (for `run-001`, the label will be `001`)
   % :type runIdx:           string
   %
-  % :param type:            datatype (``bold``, ``events``, ``physio``)
-  % :type type:             string
+  % :param suffix:            datatype (``bold``, ``events``, ``physio``)
+  % :type suffix:             string
   %
   % (C) Copyright 2020 CPP_SPM developers
 
@@ -84,13 +84,13 @@
                      'sub',  subLabel, ...
                      'task', opt.taskName, ...
                      'ses', session, ...
-                     'type', 'bold');
+                     'suffix', 'bold');
 
       query = setFields(query, opt.query);
 
       runs = bids.query(BIDS, 'runs', query);
 
-      nbRuns = size(runs, 2);
+      nbRuns = numel(runs);
 
       if nbRuns == 0
         nbRuns = 1;
@@ -101,14 +101,14 @@
 
     case 'filename'
 
-      [session, run, type] = deal(varargin{:});
+      [session, run, suffix] = deal(varargin{:});
 
       query = struct( ...
                      'sub',  subLabel, ...
                      'task', opt.taskName, ...
                      'ses', session, ...
                      'run', run, ...
-                     'type', type);
+                     'suffix', suffix);
 
       % use the extra query options specified in the options
       query = setFields(query, opt.query);