Merge pull request #1476 from oesteban/fix/issue1439-fsnative

[FIX] Bad ``fsnative`` replacement in CIfTI workflow

Author: oesteban

.circleci/config.yml

@@ -415,7 +415,7 @@ jobs:
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
                 --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
                 --ignore-aroma-denoising-errors --use-aroma \
-                --output-space T1w template fsaverage5 \
+                --output-space T1w template fsaverage5 fsnative \
                 --template-resampling-grid native \
                 --use-plugin /home/circleci/src/fmriprep/.circleci/legacy.yml \
                 --nthreads 2 --cifti-output -vv
@@ -442,7 +442,7 @@ jobs:
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
                 --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
-                --output-space T1w template fsaverage5 \
+                --output-space T1w template fsaverage5 fsnative \
                 --ignore-aroma-denoising-errors --use-aroma \
                 --template-resampling-grid native \
                 --nthreads 2 --cifti-output -vv

.circleci/ds005_outputs.txt

@@ -41,6 +41,8 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_regresso
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-MELODIC_mixing.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-L.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-R.func.gii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-L.func.gii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-R.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
@@ -59,6 +61,8 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regresso
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-L.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-R.func.gii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-L.func.gii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-R.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz

.circleci/ds005_partial_outputs.txt

@@ -41,6 +41,8 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_regresso
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-MELODIC_mixing.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-L.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-R.func.gii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-L.func.gii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-R.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz

fmriprep/cli/run.py

@@ -581,6 +581,15 @@ 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").'
+        )
+
     # Check output_space
     if 'template' not in output_spaces and (opts.use_syn_sdc or opts.force_syn):
         msg = ['SyN SDC correction requires T1 to MNI registration, but '

fmriprep/workflows/bold/base.py

@@ -779,10 +779,11 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
             ])
 
     # SURFACES ##################################################################################
-    if freesurfer and any(space.startswith('fs') for space in output_spaces):
+    surface_spaces = [space for space in output_spaces if space.startswith('fs')]
+    if freesurfer and surface_spaces:
         LOGGER.log(25, 'Creating BOLD surface-sampling workflow.')
         bold_surf_wf = init_bold_surf_wf(mem_gb=mem_gb['resampled'],
-                                         output_spaces=output_spaces,
+                                         output_spaces=surface_spaces,
                                          medial_surface_nan=medial_surface_nan,
                                          name='bold_surf_wf')
         workflow.connect([
@@ -796,18 +797,19 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
         ])
 
         # CIFTI output
-        if cifti_output and 'template' in output_spaces:
+        if cifti_output and surface_spaces:
             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')]
 
             workflow.connect([
                 (bold_surf_wf, gen_cifti, [
-                    ('targets.out', 'surface_target'),
                     ('outputnode.surfaces', 'gifti_files')]),
                 (inputnode, gen_cifti, [('subjects_dir', 'subjects_dir')]),
                 (bold_mni_trans_wf, gen_cifti, [('outputnode.bold_mni', 'bold_file')]),

fmriprep/workflows/bold/resampling.py

@@ -84,6 +84,7 @@ def init_bold_surf_wf(mem_gb, output_spaces, medial_surface_nan, name='bold_surf
             BOLD series, resampled to FreeSurfer surfaces
 
     """
+    # Ensure volumetric spaces do not sneak into this workflow
     spaces = [space for space in output_spaces if space.startswith('fs')]
 
     workflow = Workflow(name=name)