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FIX: Restore --ignore t2w/flair options #2260

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Merged
merged 1 commit into from
Sep 7, 2020
Merged

FIX: Restore --ignore t2w/flair options #2260

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4 changes: 4 additions & 0 deletions docs/workflows.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -209,6 +209,10 @@ If T1w voxel sizes are less than 1mm in all dimensions (rounding to nearest
.1mm), `submillimeter reconstruction`_ is used, unless disabled with
``--no-submm-recon``.

If T2w or FLAIR images are available, and you do not want them included in
FreeSurfer reconstruction, use ``--ignore t2w`` or ``--ignore flair``,
respectively.

``lh.midthickness`` and ``rh.midthickness`` surfaces are created in the subject
``surf/`` directory, corresponding to the surface half-way between the gray/white
boundary and the pial surface.
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2 changes: 1 addition & 1 deletion fmriprep/cli/parser.py
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Expand Up @@ -242,7 +242,7 @@ def _bids_filter(value):
action="store",
nargs="+",
default=[],
choices=["fieldmaps", "slicetiming", "sbref"],
choices=["fieldmaps", "slicetiming", "sbref", "t2w", "flair"],
help="ignore selected aspects of the input dataset to disable corresponding "
"parts of the workflow (a space delimited list)",
)
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