update MoAE code

Author: Remi-Gau

demos/MoAE/moae_01_preproc.m

@@ -6,8 +6,8 @@
 clear;
 clc;
 
-download_data = true;
-clean = true;
+download_data = false;
+clean = false;
 
 try
   run ../../initCppSpm.m;
@@ -20,12 +20,8 @@
 
 reportBIDS(opt);
 
-opt.pipeline.type = 'preproc';
-
 bidsCopyInputFolder(opt);
 
-bidsSTC(opt);
-
 bidsSpatialPrepro(opt);
 
 anatomicalQA(opt);

demos/MoAE/moae_03_create_roi_extract_data.m

@@ -16,6 +16,8 @@
 subLabel = '01';
 
 opt = moae_get_option_stats();
+opt.pipeline.type = 'stats';
+opt = checkOptions(opt);
 
 %% Get the con image to extract data
 % we can do this by using the "label-XXXX"

demos/MoAE/moae_04_slice_display.m

@@ -18,6 +18,8 @@
 subLabel = '01';
 
 opt = moae_get_option_stats();
+opt.pipeline.type = 'stats';
+opt = checkOptions(opt);
 
 use_schema = false;
 BIDS_ROI = bids.layout(opt.dir.roi, use_schema);
@@ -78,8 +80,8 @@
 
 % we reuse the details for the SPM montage
 settings.slice.orientation = opt.result.Nodes(1).Output.montage.orientation;
-settings.slice.disp_slices = -15:3:30;
-settings.fig_specs.n.slice_column = 5;
+settings.slice.disp_slices = -15:3:18;
+settings.fig_specs.n.slice_column = 4;
 settings.fig_specs.title = opt.result.Nodes(1).Contrasts(1).Name;
 
 %% Display the layers

demos/MoAE/moae_get_option_fmriprep_preproc.m

@@ -20,7 +20,6 @@
   opt.space = {'MNI152NLin2009cAsym'};
 
   opt.query.desc = {'preproc', 'confounds'};
-  %   opt.query.space = opt.space;
 
   %% DO NOT TOUCH
   opt = checkOptions(opt);

demos/MoAE/moae_get_option_stats.m

@@ -19,10 +19,6 @@
   opt.dir.roi = fullfile(opt.dir.derivatives, 'cpp_spm-roi');
   opt.dir.stats = fullfile(opt.dir.derivatives, 'cpp_spm-stats');
 
-  opt.pipeline.type = 'stats';
-
-  opt.space = {'IXI549Space'};
-
   opt.model.file = fullfile(fileparts(mfilename('fullpath')), ...
                             'models', 'model-MoAE_smdl.json');
   % to add the hrf temporal derivative = [1 0]

demos/MoAE/models/model-MoAE_smdl.json

@@ -3,7 +3,8 @@
   "BIDSModelVersion": "1.0.0",
   "Description": "contrasts to compute for the FIL MoAE dataset",
   "Input": {
-    "task": "auditory"
+    "task": "auditory",
+    "space": "IXI549Space"
   },
   "Nodes": [
     {
@@ -53,4 +54,4 @@
       ]
     }
   ]
-}
+}