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docs(segment): added **kwargs in docstrings #693

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33 changes: 31 additions & 2 deletions cortex/segment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,8 +45,17 @@ def init_subject(subject, filenames, do_import_subject=False, **kwargs):
editing) into pycortex. False by default, since we recommend editing
(or at least inspecting) the brain mask and white matter segmentations
prior to importing into pycortex.
kwargs : keyword arguments passed to cortex.freesurfer.autorecon()
useful ones: parallel=True, n_cores=4 (or more, if you have them)
**kwargs
Additional keyword arguments are forwarded to
`cortex.freesurfer.autorecon`. The deprecated `run_all` kwarg is
also accepted as an alias for `do_import_subject`.

parallel : bool, optional
Whether to run autorecon-all in parallel (only applies to the
'2', 'wm', or 'all' autorecon steps). Default True.
n_cores : int, optional
Number of cores to use for parallelization, if `parallel` is
True. Defaults to all available CPU cores.
"""
if "run_all" in kwargs:
warnings.warn(
Expand Down Expand Up @@ -193,6 +202,26 @@ def cut_surface(
auto_overwrite : bool
Whether to overwrite existing flatmaps. If True, the flatmap will be
overwritten without asking for confirmation.
**kwargs
Additional keyword arguments are forwarded to the flattening backend
selected by `flatten_with`:

save_every : int, optional
Only used when `flatten_with` is 'freesurfer'. If not None, saves
a version of the mesh every `save_every` iterations of the
flattening process (via `freesurfer.flatten`). Useful for
determining why a flattening fails.
n_iterations : int, optional
Only used when `flatten_with` is 'SLIM'. Number of iterations for
the SLIM flattening algorithm. Default is 20.
slim_path : str, optional
Only used when `flatten_with` is 'SLIM'. Path to the SLIM
executable. Defaults to the path specified in the pycortex
config file.
do_flatten : bool, optional
Only used when `flatten_with` is 'SLIM'. Whether to proceed with
flattening. If None (default), prompts for confirmation
interactively.
"""

if fs_subject is None:
Expand Down