Merge pull request #56 from Remi-Gau/remi-dev

fix problem when task JSON file is missing from root folder

Author: Remi-Gau

subfun/BIDS_copyRawFolder.m

@@ -39,15 +39,13 @@ function BIDS_copyRawFolder(opt, deleteZippedNii)
     fprintf('derivatives directory already exists. \n')
 end
 
-% make copy dataset description file from raw folder if it doesnt exist
-copyfile(fullfile(rawDir, 'dataset_description.json'), derivativeDir);
-fprintf('dataset_description.json copied to derivatives directory \n');
+% copy TSV and JSON file from raw folder if it doesnt exist
+copyfile(fullfile(rawDir, '*.json'), derivativeDir);
+fprintf(' json files copied to derivatives directory \n');
 
-% copy task json files from raw to derivatives
-copyfile(fullfile(rawDir, 'task-*_bold.json'), derivativeDir);
-fprintf('task JSON files copied to derivatives directory \n');
+copyfile(fullfile(rawDir, '*.tsv'), derivativeDir);
+fprintf(' tsv files copied to derivatives directory \n');
 
-% copy TSV files?
 
 %% Loop through the groups, subjects, sessions
 

subfun/pmCon.m

@@ -53,7 +53,7 @@
                         C = zeros(1,size(SPM.xX.X,2));
 
                         % get regressors index corresponding to the HRF of that condition
-                        [cdt_name, regIdx] = getRegIdx(Step, iCon, SPM);
+                        [cdt_name, regIdx] = getRegIdx(Step.AutoContrasts, iCon, SPM);
 
                         % give them a value of 1
                         C(end,regIdx) = 1;
@@ -80,7 +80,7 @@
                         for iCdt = 1:length(Step.Contrasts(iCon).ConditionList)
 
                             % get regressors index corresponding to the HRF of that condition
-                            [~, regIdx] = getRegIdx(Step, iCon, SPM);
+                            [~, regIdx] = getRegIdx(Step.Contrasts, iCon, SPM, iCdt);
 
                             % give them a value of 1
                             C(end,regIdx) = Step.Contrasts(iCon).weights(iCdt);
@@ -107,7 +107,7 @@
                     for iCon = 1:length(Step.AutoContrasts)
 
                         % get regressors index corresponding to the HRF of that condition
-                        [cdt_name, regIdx] = getRegIdx(Step, iCon, SPM);
+                        [cdt_name, regIdx] = getRegIdx(Step.AutoContrasts, iCon, SPM);
 
                         regIdx = find(regIdx);
 
@@ -140,11 +140,16 @@
 
 
 
-function  [cdt_name, regIdx] = getRegIdx(Step, iCon, SPM)
+function  [cdt_name, regIdx] = getRegIdx(conList, iCon, SPM, iCdt)
 % get regressors index corresponding to the HRF of of a condition
 
+if iscell(conList)
+    cdt_name = conList{iCon};
+elseif isstruct(conList)
+    cdt_name = conList(iCon).ConditionList{iCdt};
+end
+
 % get condition name
-cdt_name = Step.AutoContrasts{iCon};
 cdt_name = strrep(cdt_name, 'trial_type.', '');
 
 % get regressors index corresponding to the HRF of that condition

test/dummyData/derivatives/SPM12_CPPL/sub-01/stats/ffx_visMotion/ffx_6/SPM.mat

@@ -0,0 +1,35 @@
+{
+  "Name": "Motion localizer",
+  "Description": "contrasts for the motion localizer dataset",
+  "Input": {
+    "task": "visMotion"
+  },
+  "Steps": [
+    {
+      "Level": "subject",
+      "AutoContrasts": ["trial_type.VisMot", "trial_type.VisStat" ],
+      "Contrasts": [
+        {
+          "Name": "VisMot_gt_VisStat",
+          "ConditionList": [
+            "trial_type.VisMot", "trial_type.VisStat"
+          ],
+          "weights": [1, -1],
+          "type": "t"
+        },
+        {
+          "Name": "VisStat_gt_VisMot",
+          "ConditionList": [
+            "trial_type.VisMot", "trial_type.VisStat"
+          ],
+          "weights": [-1, 1],
+          "type": "t"
+        }
+      ]
+    },
+    {
+      "Level": "dataset",
+      "AutoContrasts": ["trial_type.VisMot", "trial_type.VisStat", "VisMot_gt_VisStat", "VisStat_gt_VisMot"]
+    }
+  ]
+}

test/dummyData/model/model-visMotionLoc_smdl.json

@@ -0,0 +1,29 @@
+function test_pmCon()
+% Small test to ensure that pmCon returns what we asked for
+
+addpath(genpath(fullfile(pwd, '..')))
+
+opt.dataDir = fullfile(pwd, 'dummyData', 'derivatives');
+opt.taskName = 'visMotion';
+opt.model.univariate.file = fullfile(pwd, 'dummyData', 'model', 'model-visMotionLoc_smdl.json');
+
+ffxDir = fullfile(opt.dataDir, 'SPM12_CPPL', 'sub-01', 'stats', 'ffx_visMotion', 'ffx_6');
+
+isMVPA = 0;
+
+contrasts = pmCon(ffxDir, opt.taskName, opt, isMVPA);
+
+
+assert(isequal(contrasts(1).name, 'VisMot'))
+assert(isequal(contrasts(1).C, [1 0 0 0 0 0 0 0 0]))
+
+assert(isequal(contrasts(2).name, 'VisStat'))
+assert(isequal(contrasts(2).C, [0 1 0 0 0 0 0 0 0]))
+
+assert(isequal(contrasts(3).name, 'VisMot_gt_VisStat'))
+assert(isequal(contrasts(3).C, [1 -1 0 0 0 0 0 0 0]))
+
+assert(isequal(contrasts(4).name, 'VisStat_gt_VisMot'))
+assert(isequal(contrasts(4).C, [-1 1 0 0 0 0 0 0 0]))
+
+end