fix(@effigies' review): address several comments not deferred to docs/revise-1596

Author: oesteban

fmriprep/cli/run.py

@@ -130,14 +130,14 @@ def get_parser():
     g_conf.add_argument(
         '--output-spaces', nargs='+', action=ParseTemplates,
         help="""\
-Paths or keywords prescribing standard spaces to which normalize the input T1w image \
-and nonstandard spaces in which BOLD runs will be resampled (valid keywords are: \
-%s and paths poing to templates) with modifiers (optional parameters).
-Output spaces may be templates with modifiers or dataset-specific references. \
-Templates take the form ``<TEMPLATE>[:res-<resolution>][:cohort-<label>][...]``,  \
-with optional, colon-separated parameters, while dataset-specific references imply \
-a specific orientation and sampling grid.\
-""" % ', '.join('"%s"' % s for s in templates() + NONSTANDARD_REFERENCES))
+Standard and non-standard spaces to resample anatomical and functional images to. \
+Standard spaces may be specified by the form \
+``<TEMPLATE>[:res-<resolution>][:cohort-<label>][...]``, where ``<TEMPLATE>`` is \
+a keyword (valid keywords: %s) or path pointing to a user-supplied template, and \
+may be followed by optional, colon-separated parameters. \
+Non-standard spaces (valid keywords: %s) imply specific orientations and sampling \
+grids""" % (', '.join('"%s"' % s for s in templates()),
+            ', '.join(NONSTANDARD_REFERENCES)))
 
     g_conf.add_argument(
         '--output-space', required=False, action='store', type=str, nargs='+',
@@ -209,7 +209,7 @@ def get_parser():
     # FreeSurfer options
     g_fs = parser.add_argument_group('Specific options for FreeSurfer preprocessing')
     g_fs.add_argument(
-        '--fs-license-file', type=Path,
+        '--fs-license-file', metavar='PATH', type=Path,
         help='Path to FreeSurfer license key file. Get it (for free) by registering'
              ' at https://surfer.nmr.mgh.harvard.edu/registration.html')
 
@@ -688,8 +688,8 @@ def parse_spaces(opts):
         if 'MNI152NLin2009cAsym' not in output_spaces:
             output_spaces['MNI152NLin2009cAsym'] = {'res': 2}
             print("""Option ``--cifti-output`` requires functional images to be resampled to \
-``MNI152NLin6Asym`` space. Such template identifier has been automatically added to the list \
-of output spaces (option "--output-space").""", file=stderr)
+``MNI152NLin2009cAsym`` space. Such template identifier has been automatically added to the \
+list of output spaces (option "--output-space").""", file=stderr)
         if not [s for s in output_spaces if s in ('fsaverage5', 'fsaverage6')]:
             output_spaces['fsaverage5'] = {}
             print("""Option ``--cifti-output`` requires functional images to be resampled to \

fmriprep/interfaces/reports.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
@@ -28,7 +26,8 @@
 \t\t<li>Structural images: {n_t1s:d} T1-weighted {t2w}</li>
 \t\t<li>Functional series: {n_bold:d}</li>
 {tasks}
-\t\t<li>Standard output spaces: {output_spaces}</li>
+\t\t<li>Standard output spaces: {std_spaces}</li>
+\t\t<li>Non-standard output spaces: {nstd_spaces}</li>
 \t\t<li>FreeSurfer reconstruction: {freesurfer_status}</li>
 \t</ul>
 """
@@ -40,7 +39,6 @@
 \t\t\t<li>Slice timing correction: {stc}</li>
 \t\t\t<li>Susceptibility distortion correction: {sdc}</li>
 \t\t\t<li>Registration: {registration}</li>
-\t\t\t<li>Functional series resampled to spaces: {output_spaces}</li>
 \t\t\t<li>Confounds collected: {confounds}</li>
 \t\t</ul>
 """
@@ -81,7 +79,8 @@ class SubjectSummaryInputSpec(BaseInterfaceInputSpec):
     bold = InputMultiObject(traits.Either(
         File(exists=True), traits.List(File(exists=True))),
         desc='BOLD functional series')
-    output_spaces = InputMultiObject(Str, desc='list of standard spaces')
+    std_spaces = InputMultiObject(Str, desc='list of standard spaces')
+    nstd_spaces = InputMultiObject(Str, desc='list of non-standard spaces')
 
 
 class SubjectSummaryOutputSpec(SummaryOutputSpec):
@@ -138,7 +137,8 @@ def _generate_segment(self):
             t2w=t2w_seg,
             n_bold=len(bold_series),
             tasks=tasks,
-            output_spaces=', '.join(self.inputs.output_spaces),
+            std_spaces=', '.join(self.inputs.std_spaces),
+            nstd_spaces=', '.join(self.inputs.nstd_spaces),
             freesurfer_status=freesurfer_status)
 
 
@@ -154,7 +154,6 @@ class FunctionalSummaryInputSpec(BaseInterfaceInputSpec):
     fallback = traits.Bool(desc='Boundary-based registration rejected')
     registration_dof = traits.Enum(6, 9, 12, desc='Registration degrees of freedom',
                                    mandatory=True)
-    output_spaces = traits.List(desc='Target spaces')
     confounds_file = File(exists=True, desc='Confounds file')
     tr = traits.Float(desc='Repetition time', mandatory=True)
 
@@ -187,7 +186,6 @@ def _generate_segment(self):
                 conflist = cfh.readline().strip('\n').strip()
         return FUNCTIONAL_TEMPLATE.format(
             pedir=pedir, stc=stc, sdc=self.inputs.distortion_correction, registration=reg,
-            output_spaces=', '.join(self.inputs.output_spaces),
             confounds=re.sub(r'[\t ]+', ', ', conflist), tr=self.inputs.tr)
 
 

fmriprep/workflows/base.py

@@ -475,8 +475,10 @@ def init_single_subject_wf(
     bids_info = pe.Node(BIDSInfo(
         bids_dir=layout.root, bids_validate=False), name='bids_info')
 
-    summary = pe.Node(SubjectSummary(output_spaces=list(std_spaces.keys())),
-                      name='summary', run_without_submitting=True)
+    summary = pe.Node(SubjectSummary(
+        std_spaces=list(std_spaces.keys()),
+        nstd_spaces=list(set(NONSTANDARD_REFERENCES).intersection(output_spaces.keys()))),
+        name='summary', run_without_submitting=True)
 
     about = pe.Node(AboutSummary(version=__version__,
                                  command=' '.join(sys.argv)),

fmriprep/workflows/bold/base.py

@@ -392,12 +392,12 @@ def init_func_preproc_wf(
     boldbuffer = pe.Node(niu.IdentityInterface(fields=['bold_file']), name='boldbuffer')
 
     summary = pe.Node(
-        FunctionalSummary(output_spaces=list(output_spaces.keys()),
-                          slice_timing=run_stc,
-                          registration='FreeSurfer' if freesurfer else 'FSL',
-                          registration_dof=bold2t1w_dof,
-                          pe_direction=metadata.get("PhaseEncodingDirection"),
-                          tr=metadata.get("RepetitionTime")),
+        FunctionalSummary(
+            slice_timing=run_stc,
+            registration='FreeSurfer' if freesurfer else 'FSL',
+            registration_dof=bold2t1w_dof,
+            pe_direction=metadata.get("PhaseEncodingDirection"),
+            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}