How to use the smriprep.interfaces.reports.SubjectSummary function in smriprep

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github poldracklab / smriprep / smriprep / workflows / base.py View on Github external
if fast_track:
        from ..utils.bids import collect_derivatives
        std_spaces = spaces.get_spaces(nonstandard=False, dim=(3,))
        deriv_cache = collect_derivatives(
            Path(output_dir) / 'smriprep', subject_id, std_spaces, freesurfer)

    inputnode = pe.Node(niu.IdentityInterface(fields=['subjects_dir']),
                        name='inputnode')

    bidssrc = pe.Node(BIDSDataGrabber(subject_data=subject_data, anat_only=True),
                      name='bidssrc')

    bids_info = pe.Node(BIDSInfo(bids_dir=layout.root), name='bids_info',
                        run_without_submitting=True)

    summary = pe.Node(SubjectSummary(output_spaces=spaces.get_spaces(nonstandard=False)),
                      name='summary', run_without_submitting=True)

    about = pe.Node(AboutSummary(version=__version__,
                                 command=' '.join(sys.argv)),
                    name='about', run_without_submitting=True)

    ds_report_summary = pe.Node(
        DerivativesDataSink(base_directory=output_dir, dismiss_entities=("session",),
                            desc='summary', datatype="figures"),
        name='ds_report_summary', run_without_submitting=True)

    ds_report_about = pe.Node(
        DerivativesDataSink(base_directory=output_dir, dismiss_entities=("session",),
                            desc='about', datatype="figures"),
        name='ds_report_about', run_without_submitting=True)
github poldracklab / smriprep / smriprep / interfaces / reports.py View on Github external
def _run_interface(self, runtime):
        if isdefined(self.inputs.subject_id):
            self._results['subject_id'] = self.inputs.subject_id
        return super(SubjectSummary, self)._run_interface(runtime)