Pass your mask to recon-all with -xmask
On 1/30/2023 1:13 AM, Boa Sorte Silva, Narlon wrote:
External Email - Use Caution
Hi there,
I just wanted to follow-up on this.
Thanks!
Nárlon Cássio
*Nárlon Cássio Boa Sorte Silva* PhD (He, Him, His)
CIHR and MSHR BC/PARF Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy, Faculty of Medicine
University of British Columbia
Vancouver, Canada
Twitter: @BoaNarlon
On Jan 18, 2023, at 7:33 PM, Boa Sorte Silva, Narlon
<narlon.si...@ubc.ca> wrote:
Dear FreeSurfer experts,
I dealing with some issues regarding skull stripping in FreeSurfer
(v7.1.1).
It seems like the conventional approaches (e.g., adjusting -wsthresh)
doesn’t seem to help. As well, applying these preprocessing steps to
the raw T1w BEFORE processing in FreeSurfer doesn’t seem to help
either. I have tried: intensity truncation, N4 bias field correction,
data normalization (with different combinations). Considering that
we’re analyzing data from a large dataset (>500 scans * multiple
timepoints), manual editing may not feasible.
Therefore, to address poor skull stripping, I was wondering if it is
possible to use a brain mask created outside FreeSurfer for the same
subject to help with skull stripping. I saw in previous emails in the
Archive that the steps below could work.
Can someone confirm if this is still true and would work for v7.1.1?
1. run recon-all (as one normally would)
2. apply mri_mask to mask the T1.mgz with external brain mask
volume (in native space)
3. name the output “brainmask.mgz” and move it to "subjid/mri/“
3. re-run recon-all starting from -autorecon2 -autorecon3
Thanks for your help!
Nárlon Cássio
Nárlon Cássio Boa Sorte Silva PhD (He, Him, His)
CIHR and MSHR BC/PARF Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy, Faculty of Medicine
University of British Columbia
Vancouver, Canada
Twitter: @BoaNarlon
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
