Merge pull request #772 from Remi-Gau/design_only

[ENH] add design only to CLI

Author: Remi-Gau

bidspm.m

@@ -16,7 +16,7 @@ function bidspm(varargin)
   isEmptyOrCellstr = @(x) isempty(x) || iscellstr(x);  %#ok<*ISCLSTR>
   isFileOrStruct = @(x) isstruct(x) || exist(x, 'file') == 2;
 
-  isLogical = @(x) islogial(x) && numel(x) == 1;
+  isLogical = @(x) islogical(x) && numel(x) == 1;
   isChar = @(x) ischar(x);
   isPositiveScalar = @(x) isnumeric(x) && numel(x) == 1 && x >= 0;
 
@@ -51,6 +51,7 @@ function bidspm(varargin)
   addParameter(args, 'preproc_dir', pwd, isFolder);
   addParameter(args, 'model_file', struct([]), isFileOrStruct);
   addParameter(args, 'roi_based', false, isLogical);
+  addParameter(args, 'design_only', false, isLogical);
   % group level stats only
   addParameter(args, 'node_name', '', isChar);
 
@@ -195,6 +196,7 @@ function bidspm(varargin)
     % stats
     opt.dir.preproc = args.Results.preproc_dir;
     opt.model.file = args.Results.model_file;
+    opt.model.designOnly = args.Results.design_only;
 
     opt = overrideRoiBased(opt, args);
 
@@ -322,16 +324,27 @@ function stats(args)
   contrasts = ismember(action, {'stats', 'contrasts'});
   results = ismember(action, {'stats', 'contrasts', 'results'});
 
+  if opt.model.designOnly
+    contrasts = false;
+    results = false;
+  end
+
   if opt.glm.roibased.do
 
     bidsFFX('specify', opt);
-    bidsRoiBasedGLM(opt);
+    if ~opt.model.designOnly
+      bidsRoiBasedGLM(opt);
+    end
 
   else
 
     if estimate
       if isSubjectLevel
-        bidsFFX('specifyAndEstimate', opt);
+        if opt.model.designOnly
+          bidsFFX('specify', opt);
+        else
+          bidsFFX('specifyAndEstimate', opt);
+        end
       else
         bidsRFX('RFX', opt, 'nodeName', nodeName);
       end

demos/MoAE/test_moae.m

@@ -47,8 +47,7 @@
 models = {fullfile(WD, 'models', 'model-MoAE_smdl.json')
           fullfile(WD, 'models', 'model-MoAE_smdl.json')
           fullfile(WD, 'models', 'model-MoAEindividual_smdl.json')
-          fullfile(WD, 'models', 'model-MoAEindividual_smdl.json')
-         };
+          fullfile(WD, 'models', 'model-MoAEindividual_smdl.json')};
 
 for iOption = 1:numel(space)
 
@@ -69,6 +68,16 @@
   %% stats
   preproc_dir = fullfile(output_dir, 'bidspm-preproc');
 
+  % only specify the subject level model
+  bidspm(bids_dir, output_dir, 'subject', ...
+         'participant_label', {'01'}, ...
+         'action', 'stats', ...
+         'preproc_dir', preproc_dir, ...
+         'model_file', models{iOption}, ...
+         'options', optionsFile, ...
+         'design_only', true);
+
+  % specify, estimate model and contrasts, and view results
   bidspm(bids_dir, output_dir, 'subject', ...
          'participant_label', {'01'}, ...
          'action', 'stats', ...

src/messages/bidspmHelp.m

@@ -136,6 +136,7 @@ function bidspmHelp()
   %           'space', {'individual', 'IXI549Space'}, ...
   %           'options', struct([]), ...,
   %           'roi_based', false, ...
+  %           'design_only', false, ...
   %           'ignore', {}, ...
   %           'task', {}, ...
   %           'fwhm', 6)
@@ -153,16 +154,20 @@ function bidspmHelp()
   % *Optional parameters*
   %
   % :param roi_based:
-  % :type  roi_based:   logical
+  % :type  roi_based:     logical
   %
   % :param task:
-  % :type  task:        cell string
+  % :type  task:          cell string
   %
-  % :param fwhm:        smoothing lelvel of the preprocessed data
-  % :type  fwhm:        positive scalar
+  % :param fwhm:          smoothing lelvel of the preprocessed data
+  % :type  fwhm:          positive scalar
+  %
+  % :param design_only:   to only run the model specification when at the group level
+  % :type  design_only:   logical
+  %
+  % :param ignore:        can be any of ``{'qa'}``
+  % :type  ignore:        cell string
   %
-  % :param ignore:      can be any of ``{'qa'}``
-  % :type  ignore:      cell string
   %
   % **low level calls**
   %