solve merge conflicts

Author: Remi-Gau

.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

.github/workflows/run_tests.yml

@@ -17,7 +17,8 @@ name: tests and coverage
 on:
   push:
     branches:
-      - master
+      - main
+      - dev
   pull_request:
     branches: '*'
 

demos/MoAE/moae_create_roi_extract_data.m

@@ -0,0 +1,59 @@
+% (C) Copyright 2021 Remi Gau
+
+%% Create ROI and extract data from it
+%
+% FYI: this is "double  dipping" as we use the same data to create the ROI
+% we are going to extract the value from.
+%
+
+run moae_run.m;
+
+subLabel = '01';
+
+saveROI = true;
+
+sphere.radius = 3;
+sphere.maxNbVoxels = 200;
+
+opt = setDerivativesDir(opt);
+ffxDir = getFFXdir(subLabel, FWHM, opt);
+
+maskImage = spm_select('FPList', ffxDir, '^.*_mask.nii$');
+
+% we get the con image to extract data
+% we can do this by using the "label-XXXX" from the mask
+p = bids.internal.parse_filename(spm_file(maskImage, 'filename'));
+conImage = spm_select('FPList', ffxDir, ['^con_' p.entities.label '.nii$']);
+
+%% Create ROI right auditory cortex
+sphere.location = [57 -22 11];
+
+specification  = struct( ...
+                        'mask1', maskImage, ...
+                        'mask2', sphere);
+
+[~, roiFile] = createRoi('expand', specification, conImage, pwd, saveROI);
+
+% rename mask image
+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
+sphere.location = [-57 -22 11];
+
+specification  = struct( ...
+                        'mask1', maskImage, ...
+                        'mask2', sphere);
+
+[~, roiFile] = createRoi('expand', specification, conImage, pwd, saveROI);
+newname.desc = 'left auditory cortex';
+leftRoiFile = renameFile(roiFile, newname);
+
+%%
+right_data = spm_summarise(conImage, rightRoiFile);
+left_data = spm_summarise(conImage, leftRoiFile);

demos/MoAE/moae_run.m

@@ -0,0 +1,55 @@
+% (C) Copyright 2019 Remi Gau
+
+% This script will download the dataset from the FIL for the block design SPM tutorial
+% and will run the basic preprocessing, FFX and contrasts on it.
+%
+% Results might be a bit different from those in the manual as some
+% default options are slightly different in this pipeline
+% (e.g use of FAST instead of AR(1), motion regressors added)
+
+clear;
+clc;
+
+% Smoothing to apply
+FWHM = 6;
+
+downloadData = true;
+
+run ../../initCppSpm.m;
+
+%% Set options
+opt = moae_get_option();
+
+download_moae_ds(downloadData);
+
+%% Run batches
+% reportBIDS(opt);
+bidsCopyRawFolder(opt, 1);
+
+% In case you just want to run segmentation and skull stripping
+% NOTE: skull stripping is also included in 'bidsSpatialPrepro'
+bidsSegmentSkullStrip(opt);
+
+bidsSTC(opt);
+
+bidsSpatialPrepro(opt);
+
+% The following do not run on octave for now (because of spmup)
+% anatomicalQA(opt);
+% bidsResliceTpmToFunc(opt);
+% functionalQA(opt);
+
+% create a whole brain functional mean image mask
+% so the mask will be in the same resolution/space as the functional images
+% one may not need it if they are running bidsFFX
+% since it creates a mask.nii by default
+opt.skullstrip.mean = 1;
+mask = bidsWholeBrainFuncMask(opt);
+
+% smoooth the funcitional images
+bidsSmoothing(FWHM, opt);
+
+% The following crash on Travis CI
+bidsFFX('specifyAndEstimate', opt, FWHM);
+bidsFFX('contrasts', opt, FWHM);
+bidsResults(opt, FWHM);

src/batches/setBatchSubjectLevelContrasts.m

@@ -23,8 +23,12 @@
 
   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;

src/batches/setBatchSubjectLevelGLMSpec.m

@@ -44,6 +44,7 @@
                           'suffix', 'bold', ...
                           'extension', '.nii');
     hdr = spm_vol(fileName{1});
+
     % we are assuming axial acquisition here
     sliceOrder = 1:hdr(1).dim(3);
   end

src/batches/setBatchSubjectLevelResults.m

@@ -39,6 +39,7 @@
   result.outputNameStructure = struct( ...
                                       'suffix', 'spmT', ...
                                       'ext', '.nii', ...
+                                      'use_schema', 'false', ...
                                       'entities', struct('sub', '', ...
                                                          'task', opt.taskName, ...
                                                          'space', opt.space, ...

src/getBoldFilename.m

@@ -0,0 +1,49 @@
+function [boldFileName, subFuncDataDir] = getBoldFilename(varargin)
+  %
+  % Get the filename and the directory of a bold file for a given session /
+  % run.
+  %
+  % Unzips the file if necessary.
+  %
+  % USAGE::
+  %
+  %   [boldFileName, subFuncDataDir] = getBoldFilename(BIDS, subID, sessionID, runID, opt)
+  %
+  % :param BIDS:        returned by bids.layout when exploring a BIDS data set.
+  % :type BIDS:         structure
+  % :param subID:       label of the subject ; in BIDS lingo that means that for a file name
+  %                     ``sub-02_task-foo_bold.nii`` the subID will be the string ``02``
+  % :type subID:        string
+  % :param sessionID:   session label (for `ses-001`, the label will be `001`)
+  % :type sessionID:    string
+  % :param runID:       run index label (for `run-001`, the label will be `001`)
+  % :type runID:        string
+  % :param opt:         Mostly used to find the task name.
+  % :type opt:          structure
+  %
+  %
+  % :returns: - :boldFileName: (string)
+  %           - :subFuncDataDir: (string)
+  %
+  %
+  % (C) Copyright 2020 CPP_SPM developers
+
+  [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');
+
+  % get fullpath of the file
+  % ASSUMPTION: the first file is the right one.
+  boldFileName = unzipImgAndReturnsFullpathName(boldFileName);
+
+  [subFuncDataDir, boldFileName, ext] = spm_fileparts(boldFileName);
+  boldFileName = [boldFileName ext];
+
+end

src/reports/copyFigures.m

@@ -24,7 +24,7 @@ function copyFigures(BIDS, opt, subLabel)
     runs = bids.query(BIDS, 'runs', ...
                       'sub', subLabel, ...
                       'task', opt.taskName, ...
-                      'type', 'bold');
+                      'suffix', 'bold');
 
     nbRuns = size(runs, 2);
     if nbRuns == 0

src/reports/reportBIDS.m

@@ -17,6 +17,10 @@ function reportBIDS(opt)
   %
   % (C) Copyright 2020 CPP_SPM developers
 
+  warning('bidsReport is broken and waiting for a fix on the bids-matlab side.');
+
+  return
+
   bids.report(opt.dir.raw);
 
 end