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

Jump to bottom

Brainmask incorrectly applied to externally-initiated FreeSurfer #200

Open
effigies opened this issue Jun 5, 2020 · 0 comments
Open

Brainmask incorrectly applied to externally-initiated FreeSurfer #200

effigies opened this issue Jun 5, 2020 · 0 comments
Labels
bug Something isn't working freesurfer FreeSurfer related improvements and issues
Milestone
0.11.2

Comments

@effigies
Copy link
Member

effigies commented Jun 5, 2020

While working on #154, I skipped the FreeSurfer skull-strip in favor of ours.

Screenshot from 2020-06-05 13-43-35

It looks like our brainmask injection assumes that the T1.mgz and T1w.nii.gz are in register. The t1w2fsnative_xfm is not used for this step:

https://github.com/poldracklab/smriprep/blob/d8fe13da52690b7cf2edd71f6ec38c4d660bd405/smriprep/workflows/surfaces.py#L201-L217

This is not blocking on #154, so I will just run FreeSurfer's skull-strip and continue on there.
@effigies effigies added bug Something isn't working freesurfer FreeSurfer related improvements and issues labels Jun 5, 2020
@oesteban oesteban modified the milestones: 0.7.0, 0.6.3 Jun 11, 2020
@mgxd mgxd mentioned this issue Jun 12, 2020
Merged
@effigies effigies modified the milestones: 0.6.3, 0.11.2 Apr 4, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working freesurfer FreeSurfer related improvements and issues
Projects
None yet
Milestone
0.11.2
Development

No branches or pull requests
2 participants
@effigies @oesteban