fix visMotion demo

Author: Remi-Gau

demos/vismotion/batch.m

@@ -7,35 +7,49 @@
 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')));
+addpath(genpath(fullfile(WD, '..', '..', 'src')));
+addpath(genpath(fullfile(WD, '..', '..', 'lib')));
 
 %% Run batches
 opt = getOption();
 
 checkDependencies();
 
-% copy raw folder into derivatives folder
-% BIDS_copyRawFolder(opt, 1)
+reportBIDS(opt);
 
-% preprocessing
-% BIDS_STC(opt);
-% BIDS_SpatialPrepro(opt);
-% BIDS_Smoothing(6, opt);
+bidsCopyRawFolder(opt, 1);
+% 
+% % preprocessing
+bidsSTC(opt);
+bidsSpatialPrepro(opt);
+
+% Quality control
+anatomicalQA(opt);
+
+% Not implemented yet
+% bidsResliceTpmToFunc(opt);
+% functionalQA(opt);
+
+funcFWHM = 6;
+bidsSmoothing(funcFWHM, opt);
 
 % subject level Univariate
-% BIDS_FFX(1, 6, opt);
-% BIDS_FFX(2, 6, opt);
+bidsFFX('specifyAndEstimate', opt, funcFWHM);
+bidsFFX('contrasts', opt, funcFWHM);
 
 % group level univariate
-BIDS_RFX(1, 6, 6);
-BIDS_RFX(2, 6, 6);
+conFWHM = 6;
+bidsRFX('smoothContrasts', funcFWHM, conFWHM, opt);
 
-BIDS_Results(6, 6, opt, 0);
+% Not implemented yet
+% bidsRFX('RFX', funcFWHM, conFWHM, opt);
 
+% Not implemented yet
 % subject level multivariate
-% isMVPA=1;
-% BIDS_FFX(1, 6, opt, isMVPA);
-% BIDS_FFX(2, 6, opt, isMVPA);
-% make4Dmaps(6,opt)
+% opt.model.file = fuufile(WD, ...
+%                          'models', ...
+%                          'model-motionDecodingMultivariate_smdl.json');
+% 
+% bidsFFX('specifyAndEstimate', opt, funcFWHM);
+% bidsFFX('contrasts', opt, funcFWHM);
+% concatBetaImgTmaps(funcFWHM, opt);

demos/vismotion/getOption.m

@@ -13,11 +13,12 @@
   opt.taskName = 'visMotion';
 
   % The directory where the data are located
-  opt.dataDir = '/home/remi/BIDS/visMotion/derivatives/';
+  opt.dataDir = '/home/remi/gin/CPP_visMotion/raw';
+  opt.derivativesDir = '/home/remi/Documents';
 
   % specify the model file that contains the contrasts to compute
   opt.model.file = ...
-      '/home/remi/github/CPP_BIDS_SPM_pipeline/model-visMotionLoc_smdl.json';
+      '/home/remi/github/CPP_BIDS_SPM_pipeline/demos/vismotion/models/model-visMotionLoc_smdl.json';
 
   % specify the result to compute
   % Contrasts.Name has to match one of the contrast defined in the model json file

demos/vismotion/models/model-visMotionLoc_smdl.json

@@ -5,18 +5,22 @@
     "task": "visMotion"
   },
   "Steps": [
+    {
+      "Level": "run",
+      "Model": {
+        "X": [
+          "trial_type.VisMot",
+          "trial_type.VisStat",
+          "trans_x", "trans_y", "trans_z", "rot_x", "rot_y", "rot_z"
+        ]
+      }
+    },
     {
       "Level": "subject",
       "Model": {
         "X": [
-          "trial_type.Vis_U",
-          "trial_type.Vis_D",
-          "trial_type.Vis_R",
-          "trial_type.Vis_L",
-          "trial_type.Aud_U",
-          "trial_type.Aud_D",
-          "trial_type.Aud_L",
-          "trial_type.Aud_R",
+          "trial_type.VisMot",
+          "trial_type.VisStat",
           "trans_x", "trans_y", "trans_z", "rot_x", "rot_y", "rot_z"
         ]
       },
@@ -42,7 +46,11 @@
     },
     {
       "Level": "dataset",
-      "AutoContrasts": ["trial_type.VisMot", "trial_type.VisStat", "VisMot_gt_VisStat", "VisStat_gt_VisMot"]
+      "AutoContrasts": [
+        "trial_type.VisMot", 
+        "trial_type.VisStat", 
+        "VisMot_gt_VisStat", 
+        "VisStat_gt_VisMot"]
     }
   ]
 }