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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
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.silva@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
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.silva@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 -autorecon3Thanks 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@nmr.mgh.harvard.edu
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Boa Sorte Silva, Narlon -
Douglas N. Greve