Merge pull request #2260 from effigies/fix/ignore_t2w_flair

FIX: Restore --ignore t2w/flair options

Author: mgxd

docs/workflows.rst

@@ -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.

fmriprep/cli/parser.py

@@ -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)",
     )