Merge pull request #394 from Remi-Gau/parallel

remove parfor from spatial processing and add QA options

Author: Remi-Gau

src/QA/functionalQA.m

@@ -97,7 +97,12 @@ function functionalQA(opt)
 
         outputFiles = spmup_first_level_qa( ...
                                            funcImage, ...
-                                           'Voltera', 'on', ...
+                                           'MotionParameters', opt.QA.func.Motion, ...
+                                           'FramewiseDisplacement', opt.QA.func.FD, ...
+                                           'Globals', opt.QA.func.Globals, ...
+                                           'Movie', opt.QA.func.Movie, ...
+                                           'Basics', opt.QA.func.Basics, ...
+                                           'Voltera', opt.QA.func.Voltera, ...
                                            'Radius', anatQA.avgDistToSurf);
 
         movefile( ...
@@ -122,7 +127,7 @@ function functionalQA(opt)
 
         % horrible hack to prevent the "abrupt" way spmup_volumecorr crashes
         % if nansum is not there
-        if exist('nansum', 'file') == 2
+        if opt.QA.func.carpetPlot && exist('nansum', 'file') == 2
           spmup_timeseriesplot(funcImage, TPMs(1, :), TPMs(2, :), TPMs(3, :), ...
                                'motion', 'on', ...
                                'nuisances', 'on', ...

src/defaults/checkOptions.m

@@ -57,7 +57,17 @@
   %         if you know the order in which slices were acquired, you should be able to recompute
   %         slice timing and add it to the json files in your BIDS data set.
   %     -  ``opt.glm.roibased.do``
-  %     -  ``opt.glm.QA.do = true`` - If set to ``true`` the residual images of a
+  %     -  ``opt.QA.func.carpetPlot = true`` to plot carpet plot when running ``functionaQA``
+  %     -  ``opt.QA.func`` contains a lot of options used by ``spmup_first_level_qa``
+  %         in ``functionaQA``
+  %     -  ``opt.QA.func.MotionParameters = 'on'``
+  %     -  ``opt.QA.func.FramewiseDisplacement = 'on'``
+  %     -  ``opt.QA.func.Voltera = 'on'``
+  %     -  ``opt.QA.func.Globals = 'on'``
+  %     -  ``opt.QA.func.Movie = 'on'`` ; set it to ``off`` to skip generating movies
+  %         of the time series
+  %     -  ``opt.QA.func.Basics = 'on'``
+  %     -  ``opt.QA.glm.do = true`` - If set to ``true`` the residual images of a
   %         GLM at the subject levels will be used to estimate if there is any remaining structure
   %         in the GLM residuals (the power spectra are not flat) that could indicate
   %         the subject level results are likely confounded (see
@@ -134,7 +144,15 @@
   fieldsToSet.model.hrfDerivatives = [0 0];
   fieldsToSet.contrastList = {};
 
-  fieldsToSet.glm.QA.do = true;
+  fieldsToSet.QA.glm.do = true;
+  fieldsToSet.QA.func.carpetPlot = true;
+  fieldsToSet.QA.func.Motion = 'on';
+  fieldsToSet.QA.func.FD = 'on';
+  fieldsToSet.QA.func.Voltera = 'on';
+  fieldsToSet.QA.func.Globals = 'on';
+  fieldsToSet.QA.func.Movie = 'on';
+  fieldsToSet.QA.func.Basics = 'on';
+
   fieldsToSet.glm.roibased.do = false;
 
   % specify the results to compute

src/workflows/bidsFFX.m

@@ -85,7 +85,7 @@ function bidsFFX(action, opt, funcFWHM)
 
         saveAndRunWorkflow(matlabbatch, batchName, opt, subLabel);
 
-        if opt.glm.QA.do
+        if opt.QA.glm.do
           plot_power_spectra_of_GLM_residuals( ...
                                               getFFXdir(subLabel, funcFWHM, opt), ...
                                               opt.metadata.RepetitionTime);

src/workflows/bidsSpatialPrepro.m

@@ -47,7 +47,7 @@ function bidsSpatialPrepro(opt)
   opt.orderBatches.skullStripping = 6;
   opt.orderBatches.skullStrippingMask = 7;
 
-  parfor iSub = 1:numel(opt.subjects)
+  for iSub = 1:numel(opt.subjects)
 
     matlabbatch = {};
 

tests/utils/defaultOptions.m

@@ -35,7 +35,15 @@
 
   expectedOptions.contrastList = {};
 
-  expectedOptions.glm.QA.do = true;
+  expectedOptions.QA.glm.do = true;
+  expectedOptions.QA.func.carpetPlot = true;
+  expectedOptions.QA.func.Motion = 'on';
+  expectedOptions.QA.func.FD = 'on';
+  expectedOptions.QA.func.Voltera = 'on';
+  expectedOptions.QA.func.Globals = 'on';
+  expectedOptions.QA.func.Movie = 'on';
+  expectedOptions.QA.func.Basics = 'on';
+
   expectedOptions.glm.roibased.do = false;
 
   expectedOptions.model.file = '';