Skip to content

Wrong T1w mask used for EPI-T1 registration? #35

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
Open
chrisgorgo opened this issue Mar 3, 2018 · 2 comments
Open

Wrong T1w mask used for EPI-T1 registration? #35

chrisgorgo opened this issue Mar 3, 2018 · 2 comments
Labels
effort:high Estimated high effort task impact:medium Estimated medium impact task mp2rage problems derived from multi-echo T1w images skull-stripping Brain extraction problems

Comments

@chrisgorgo
Copy link

The T1w mask on bbr coregisration plot looks bad
image
ds000221/reportlets/fmriprep/sub-010251/ses-01/func/sub-010251_ses-01_task-rest_acq-AP_run-01_bold_bbr.svg

Even though it's good on the T1w mask plot
image
s000221/reportlets/fmriprep/sub-010251/ses-01/anat/sub-010251_ses-01_acq-mp2rage_T1w_seg_brainmask.svg
@oesteban oesteban transferred this issue from nipreps/fmriprep Jan 8, 2019
@nipreps nipreps deleted a comment from stale bot Jan 8, 2019
@oesteban oesteban added mp2rage problems derived from multi-echo T1w images skull-stripping Brain extraction problems labels Jan 8, 2019
@franklin-feingold franklin-feingold added effort:high Estimated high effort task impact:medium Estimated medium impact task labels Mar 12, 2019
@oesteban
Copy link
Member

Duplicate of #18 - follow up there.

@effigies
Copy link
Member

I don't think that is a duplicate. In this case there was a good mask, but it wasn't applied correctly in FreeSurfer. I think I remember us finding an issue with the T1w-fsnative transform since this issue was created, so it would be worth re-running this subject and seeing if it's still valid.

@oesteban oesteban reopened this Mar 10, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
effort:high Estimated high effort task impact:medium Estimated medium impact task mp2rage problems derived from multi-echo T1w images skull-stripping Brain extraction problems
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
4 participants
@effigies @chrisgorgo @oesteban @franklin-feingold