fix bugs

Author: Remi-Gau

demos/bayes/ds000114_run.m

@@ -6,17 +6,17 @@
 addpath(fullfile(pwd, '..', '..'));
 bidspm();
 
+VERBOSITY = 2;
+
+FWHM = 8;
+
 % set to false to not re run the smoothing
 SMOOTH = true;
 
 % set to false to not re run the model specification
 FIRST_LEVEL = true;
 
-VERBOSITY = 1;
-
-FWHM = 8;
-
-% to run on fewer subjects
+% set to true to run on fewer subjects and fewer models
 TESTING = true;
 
 % The directory where the data are located
@@ -56,9 +56,9 @@
 multiverse.non_steady_state = {false, true};
 
 if TESTING
-  multiverse.motion = {'none', 'basic'};
-  multiverse.wm_csf = {'none'};
-  multiverse.non_steady_state = {false};
+  multiverse.motion = {'basic', 'full'};
+  multiverse.scrub = {false, true};
+  multiverse.non_steady_state = {true};
 end
 
 createModelFamilies(default_model_file, multiverse, models_dir);
@@ -69,6 +69,9 @@
 %% Subject level analysis
 if FIRST_LEVEL
 
+  % Silence this warning as this dataset has not been slice time corrected.
+  warning('OFF', 'setBatchSubjectLevelGLMSpec:noSliceTimingInfoForGlm');
+
   bidspm(bids_dir, output_dir, 'subject', ...
          'participant_label', participant_label, ...
          'action', 'specify_only', ...

src/bids_model/addConfoundsToDesignMatrix.m

@@ -208,7 +208,9 @@
       strategy.(strategies{i}) = {strategy.(strategies{i})};
     end
 
-    if isnan(strategy.(strategies{i}){1})
+    if ~isempty(strategy.(strategies{i})) && ...
+        isnumeric(strategy.(strategies{i}){1}) && ...
+        isnan(strategy.(strategies{i}){1})
       strategy.(strategies{i}){1} = tmp.(strategies{i});
     end
 

tests/tests_bids_model/test_addConfoundsToDesignMatrix.m

@@ -7,6 +7,25 @@
   initTestSuite;
 end
 
+function test_addConfoundsToDesignMatrix_default()
+
+  bm = BidsModel('init', true);
+
+  bm = addConfoundsToDesignMatrix(bm);
+  assertEqual(numel(bm.Nodes{1}.Model.X), 0);
+
+  strategy.strategies = {'motion', 'non_steady_state'};
+  strategy.motion = 'basic';
+  strategy.non_steady_state = true;
+
+  bm = addConfoundsToDesignMatrix(bm, 'strategy', strategy);
+  assertEqual(numel(bm.Nodes{1}.Model.X), 3);
+  assertEqual(ismember({'rot_?', 'trans_?', 'non_steady_state_outlier*'}, ...
+                       bm.Nodes{1}.Model.X), ...
+              true(1, 3));
+
+end
+
 function test_addConfoundsToDesignMatrix_from_file()
 
   modelFile = fullfile(getTestDataDir(), 'models', ...
@@ -83,25 +102,6 @@ function test_addConfoundsToDesignMatrix_update_name()
   assertEqual(bm.Nodes{1}.Name, [nameBefore '_rp-full_scrub-1_tissue-full_nsso-1']);
 end
 
-function test_addConfoundsToDesignMatrix_default()
-
-  bm = BidsModel('init', true);
-
-  bm = addConfoundsToDesignMatrix(bm);
-  assertEqual(numel(bm.Nodes{1}.Model.X), 0);
-
-  strategy.strategies = {'motion', 'non_steady_state'};
-  strategy.motion = 'basic';
-  strategy.non_steady_state = true;
-
-  bm = addConfoundsToDesignMatrix(bm, 'strategy', strategy);
-  assertEqual(numel(bm.Nodes{1}.Model.X), 3);
-  assertEqual(ismember({'rot_?', 'trans_?', 'non_steady_state_outlier*'}, ...
-                       bm.Nodes{1}.Model.X), ...
-              true(1, 3));
-
-end
-
 function test_addConfoundsToDesignMatrix_warning()
 
   if bids.internal.is_octave()