add design only option to cli

Author: Remi-Gau

bidspm.m

@@ -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

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**
   %