Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

DOC: skull stripping is forced by default #2345

Merged
merged 8 commits into from
Dec 9, 2020
Merged

DOC: skull stripping is forced by default #2345

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
4eb5443
update docs, skull stripping is forced by default
jsmentch Dec 9, 2020
415aa9b
Update .zenodo.json
jsmentch Dec 9, 2020
c3bd443
Update docs/workflows.rst
jsmentch Dec 9, 2020
f0b3e43
undo update to .zenodo.json
jsmentch Dec 9, 2020
1656740
update contributors
jsmentch Dec 9, 2020
e0fd7dd
fix linebreaks docs/workflows.rst
jsmentch Dec 9, 2020
6a02ab3
Update docs/workflows.rst
jsmentch Dec 9, 2020
f74cd6b
fix spacing, indent
jsmentch Dec 9, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions .maint/contributors.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -114,6 +114,12 @@
"name": "Ma, Feilong",
"orcid": "0000-0002-6838-3971"
},
{
"affiliation": "Speech & Hearing Bioscience & Technology Program, Harvard University",
"name": "Mentch, Jeff",
"orcid": "0000-0002-7762-8678",
"type": "Researcher"
},
{
"affiliation": "Department of Psychology, Stanford University",
"name": "Moodie, Craig A.",
Expand Down
9 changes: 4 additions & 5 deletions docs/workflows.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -60,15 +60,14 @@ single reference template (see `Longitudinal processing`_).
as if they are unprocessed.
In the case of brain-extracted (skull-stripped) T1w images, attempting to perform
brain extraction again will often have poor results and may cause *fMRIPrep* to crash.
By default, *fMRIPrep* will attempt to detect these cases using a heuristic to check if the
*fMRIPrep* can attempt to detect these cases using a heuristic to check if the
T1w image is already masked.
This must be explicitly requested with ``---skull-strip-t1w auto``.
If this heuristic fails, and you know your images are skull-stripped, you can skip brain
extraction with ``--skull-strip-t1w skip``.
Likewise, if you know your images are not skull-stripped and the heuristic incorrectly
determines that they are, you can force skull stripping with ``--skull-strip-t1w force``.
The default behavior of detecting pre-extracted brains may be explicitly requested with
``---skull-strip-t1w auto``, which will use a heuristic to check if each image is
already masked.
determines that they are, you can force skull stripping with ``--skull-strip-t1w force``,
which is the current default behavior.

See also *sMRIPrep*'s
:py:func:`~smriprep.workflows.anatomical.init_anat_preproc_wf`.
Expand Down