[ENH] Code revision of anatomical workflows #622
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8 tasks
effigies
reviewed
Jul 29, 2017
fmriprep/interfaces/freesurfer.py
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| class FSInjectBrainExtractedOutputSpec(TraitedSpec): | ||
| subjects_dir = Directory(desc='FreeSurfer SUBJECTS_HOME') |
fmriprep/interfaces/freesurfer.py
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| class FSInjectBrainExtractedInputSpec(BaseInterfaceInputSpec): | ||
| subjects_dir = Directory(mandatory=True, desc='FreeSurfer SUBJECTS_HOME') |
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| # https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon | ||
| mris_inflate = '-n 50' if hires else None | ||
| return (t2w, hires, mris_inflate) |
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Is there any reason to keep these functions separate from the interfaces? The functions themselves don't make a lot of sense to use except in a pipeline (the latter especially), so there's not much need to preserve them for other uses.
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It is generally easier to write unit tests on these split functions, if we find the time. Other than that, I don't have a particular preference.
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@effigies still considering to move the code into the interfaces? Otherwise, this is ready to merge.
fmriprep/workflows/anatomical.py
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| return workflow | ||
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| def init_gifti_surface_wf(name='gifti_surface_wf'): | ||
| """ | ||
| Extract surfaces from FreeSurfer derivatives folder and | ||
| re-center GIFTI coordinates to fit align to native T1 space |
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Typo in the old docstring. Remove fit.
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Part of #225 , depends on #621
n_procsatNodeinitialization.