series of small fixes after testing pipeline on demo

Author: Remi-Gau

demo/batch_download_run.m

@@ -18,6 +18,7 @@
 WD = fileparts(mfilename('fullpath'));
 
 % we add all the subfunctions that are in the sub directories
+addpath(fullfile(WD, '..'));
 addpath(genpath(fullfile(WD, '..', 'src')));
 addpath(genpath(fullfile(WD, '..', 'lib')));
 
@@ -66,7 +67,7 @@
 %% Get data
 % fprintf('%-40s:', 'Downloading dataset...');
 % urlwrite(URL, 'MoAEpilot.zip');
-% unzip('MoAEpilot.zip', fullfile(WD, 'output'));
+unzip('MoAEpilot.zip', fullfile(WD, 'output'));
 
 %% Check dependencies
 % If toolboxes are not in the MATLAB Directory and needed to be added to
@@ -81,10 +82,12 @@
 checkDependencies();
 
 %% Run batches
+isMVPA = 0;
+
 bidsCopyRawFolder(opt, 1);
 bidsSTC(opt);
 bidsSpatialPrepro(opt);
 bidsSmoothing(FWHM, opt);
-bidsFFX(1, FWHM, opt, 0);
-bidsFFX(2, FWHM, opt, 0);
-bidsResults(FWHM, [], opt, 0);
+bidsFFX('specifyAndEstimate', opt, FWHM, isMVPA);
+bidsFFX('contrasts', opt, FWHM, isMVPA);
+bidsResults(opt, FWHM, [], isMVPA);

src/specifyContrasts.m

@@ -39,15 +39,15 @@
 
         switch Step.Level
 
-            case 'subject'
+            case 'run'
 
                 [contrasts,  con_counter] = ...
-                    specifySubjectLevelContrasts(Step, con_counter, SPM);
+                    specifyRunLvlContrasts(contrasts, Step, con_counter, SPM);
 
-            case 'run'
+            case 'subject'
 
                 [contrasts,  con_counter] = ...
-                    specifyRunLevelContrasts(Step, con_counter, SPM);
+                    specifySubLvlContrasts(contrasts, Step, con_counter, SPM);
 
         end
 
@@ -73,7 +73,7 @@
 
 end
 
-function [contrasts,  con_counter] = specifySubjectLevelContrasts(Step, con_counter, SPM)
+function [contrasts,  con_counter] = specifySubLvlContrasts(contrasts, Step, con_counter, SPM)
 
     if isfield(Step, 'AutoContrasts')
 
@@ -129,7 +129,7 @@
 
 end
 
-function [contrasts,  con_counter] = specifyRunLevelContrasts(Step, con_counter, SPM)
+function [contrasts,  con_counter] = specifyRunLvlContrasts(contrasts, Step, con_counter, SPM)
 
     if isfield(Step, 'AutoContrasts')
 

src/spmBatching/bidsResults.m

@@ -1,4 +1,4 @@
-function bidsResults(funcFWHM, conFWHM, opt, isMVPA)
+function bidsResults(opt, funcFWHM, conFWHM, isMVPA)
     % This scripts computes the results for a series of contrast that can be
     % specified at the run, subject or dataset step level (see contrast specification
     % following the BIDS stats model specification)
@@ -28,9 +28,9 @@ function bidsResults(funcFWHM, conFWHM, opt, isMVPA)
             switch opt.result.Steps(iStep).Level
 
                 case 'run'
-                    error('run level not implemented yet');
+                    warning('run level not implemented yet');
 
-                    saveMatlabBatch(matlabbatch, 'computeFfxResults', opt, subID); %#ok<UNRCH>
+                    % saveMatlabBatch(matlabbatch, 'computeFfxResults', opt, subID);
 
                 case 'subject'
 
@@ -44,7 +44,10 @@ function bidsResults(funcFWHM, conFWHM, opt, isMVPA)
                         iStep, ...
                         iCon);
 
-                    saveMatlabBatch(matlabbatch, 'computeFfxResults', opt, subID);
+                    % TODO
+                    % Save this batch in for each subject and not once for all
+
+                    saveMatlabBatch(matlabbatch, 'computeFfxResults', opt);
 
                 case 'dataset'
 
@@ -60,7 +63,7 @@ function bidsResults(funcFWHM, conFWHM, opt, isMVPA)
                     matlabbatch = resultsMatlabbatch( ...
                         matlabbatch, opt, iStep, iCon, results);
 
-                    saveMatlabBatch(matlabbatch, 'computeFfxResults', opt);
+                    saveMatlabBatch(matlabbatch, 'computeRfxResults', opt);
 
             end
         end

src/spmBatching/bidsSTC.m

@@ -49,15 +49,17 @@ function bidsSTC(opt)
             %% GET FUNCTIOVAL FILES
             fprintf(1, ' BUILDING STC JOB : STC\n');
 
-            matlabbatch = setBatchSTC(BIDS, subID, opt);
+            matlabbatch = setBatchSTC(BIDS, opt, subID);
 
             % The following lines are commented out because those parameters
             % can be set in the spm_my_defaults.m
             % matlabbatch{1}.spm.temporal.st.prefix = spm_get_defaults('slicetiming.prefix');
 
-            saveMatlabBatch(matlabbatch, 'STC', opt, subID);
+            if ~isempty(matlabbatch)
+                saveMatlabBatch(matlabbatch, 'STC', opt, subID);
 
-            spm_jobman('run', matlabbatch);
+                spm_jobman('run', matlabbatch);
+            end
 
         end
     end

src/spmBatching/bidsSmoothing.m

@@ -20,9 +20,11 @@ function bidsSmoothing(funcFWHM, opt)
 
             subID = group(iGroup).subNumber{iSub};
 
+            printProcessingSubject(groupName, iSub, subID);
+
             fprintf(1, 'PREPARING: SMOOTHING JOB \n');
 
-            matlabbatch = setBatchSmoothing(BIDS, subID, opt, funcFWHM, groupName);
+            matlabbatch = setBatchSmoothing(BIDS, opt, subID, funcFWHM);
 
             saveMatlabBatch(matlabbatch, 'Smoothing', opt, subID);
 

src/spmBatching/setBatchSTC.m

@@ -1,4 +1,4 @@
-function matlabbatch = setBatchSTC(BIDS, subID, opt)
+function matlabbatch = setBatchSTC(BIDS, opt, subID)
     % Slice timing units is in milliseconds to be BIDS compliant and not in slice number
     % as is more traditionally the case with SPM.
     %
@@ -13,6 +13,8 @@
     %
     % See README.md for more information about slice timing correction
 
+    matlabbatch = [];
+
     % get slice order
     sliceOrder = getSliceOrder(opt, 1);
     if isempty(sliceOrder)
@@ -50,8 +52,6 @@
 
     [sessions, nbSessions] = getInfo(BIDS, subID, opt, 'Sessions');
 
-    matlabbatch = [];
-
     for iSes = 1:nbSessions
 
         % get all runs for that subject across all sessions

src/spmBatching/setBatchSmoothing.m

@@ -1,4 +1,4 @@
-function matlabbatch = setBatchSmoothing(BIDS, subID, opt, funcFWHM, groupName)
+function matlabbatch = setBatchSmoothing(BIDS, opt, subID, funcFWHM)
 
     % creates prefix to look for
     prefix = getPrefix('smoothing', opt);
@@ -23,8 +23,6 @@
         % numRuns = group(iGroup).numRuns(iSub);
         for iRun = 1:nbRuns
 
-            printProcessingRun(groupName, iSub, subID, iSes, iRun);
-
             % get the filename for this bold run for this task
             [fileName, subFuncDataDir] = getBoldFilename( ...
                 BIDS, ...

src/spmBatching/setBatchSubjectLevelGLMSpec.m

@@ -75,14 +75,14 @@
         for iRun = 1:nbRuns
 
             % get functional files
-            [fullpathBoldFileName, prefix] = ...
+            fullpathBoldFileName = ...
                 getBoldFilenameForFFX(BIDS, opt, subID, funcFWHM, iSes, iRun);
             matlabbatch{1}.spm.stats.fmri_spec.sess(sesCounter).scans = ...
                 cellstr(fullpathBoldFileName);
 
             % get stimuli onset time file
             fullpathOnsetFileName = ...
-                createAndReturnOnsetFile(opt, subID, funcFWHM, boldFileName, isMVPA);
+                createAndReturnOnsetFile(opt, subID, funcFWHM, fullpathBoldFileName, isMVPA);
 
             matlabbatch{1}.spm.stats.fmri_spec.sess(sesCounter).multi = ...
                 cellstr(fullpathOnsetFileName);