Merge pull request #1514 from poldracklab/oesteban-patch-2

FIX: Make sure ``--cifti-output`` requires at least one of ``fsaverage{5,6}``

Author: oesteban

fmriprep/cli/run.py

@@ -573,7 +573,12 @@ def build_workflow(opts, retval):
       * Run identifier: {uuid}.
     """.format
 
-    output_spaces = opts.output_space or []
+    # Reduce to unique space identifiers
+    output_spaces = sorted(set(opts.output_space))
+
+    # If FS is not run, drop all fs* output spaces
+    if not opts.run_reconall:
+        output_spaces = [item for item in output_spaces if not item.startswith('fs')]
 
     # Validity of some inputs
     # ERROR check if use_aroma was specified, but the correct template was not
@@ -586,14 +591,19 @@ def build_workflow(opts, retval):
             'spaces (option "--output-space").'
         )
 
-    if opts.cifti_output and (opts.template != 'MNI152NLin2009cAsym' or
-                              'template' not in output_spaces):
-        output_spaces.append('template')
-        logger.warning(
-            'Option "--cifti-output" requires functional images to be resampled to MNI space. '
-            'The argument "template" has been automatically added to the list of output '
-            'spaces (option "--output-space").'
-        )
+    if opts.cifti_output:
+        if 'template' not in output_spaces:
+            output_spaces.append('template')
+            logger.warning(
+                'Option "--cifti-output" requires functional images to be resampled to MNI '
+                'space. The argument "template" has been automatically added to the list of '
+                'output spaces (option "--output-space").')
+        if not [s for s in output_spaces if s in ('fsaverage5', 'fsaverage6')]:
+            output_spaces = sorted(output_spaces + ['fsaverage5'])
+            logger.warning(
+                'Option "--cifti-output" requires functional images to be resampled to fsaverage '
+                'space. The argument "fsaverage5" has been automatically added to the list of '
+                'output spaces (option "--output-space").')
 
     # Check output_space
     if 'template' not in output_spaces and (opts.use_syn_sdc or opts.force_syn):

fmriprep/workflows/bold/base.py

@@ -365,6 +365,9 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
                           tr=metadata.get("RepetitionTime")),
         name='summary', mem_gb=DEFAULT_MEMORY_MIN_GB, run_without_submitting=True)
 
+    # CIfTI output: currently, we only support fsaverage{5,6}
+    cifti_spaces = [s for s in output_spaces if s in ('fsaverage5', 'fsaverage6')]
+    cifti_output = cifti_output and cifti_spaces
     func_derivatives_wf = init_func_derivatives_wf(output_dir=output_dir,
                                                    output_spaces=output_spaces,
                                                    template=template,
@@ -798,17 +801,15 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
             (bold_surf_wf, outputnode, [('outputnode.surfaces', 'surfaces')]),
         ])
 
-        # CIFTI output
-        if cifti_output and surface_spaces:
+        if cifti_output:
             bold_surf_wf.__desc__ += """\
 *Grayordinates* files [@hcppipelines], which combine surface-sampled
 data and volume-sampled data, were also generated.
 """
             gen_cifti = pe.MapNode(GenerateCifti(), iterfield=["surface_target", "gifti_files"],
                                    name="gen_cifti")
             gen_cifti.inputs.TR = metadata.get("RepetitionTime")
-            gen_cifti.inputs.surface_target = [s for s in surface_spaces
-                                               if s.startswith('fsaverage')]
+            gen_cifti.inputs.surface_target = cifti_spaces
 
             workflow.connect([
                 (bold_surf_wf, gen_cifti, [