Dear Narlon, I believe you can add -xmask [mask_volume_file] to your recon-all command. To generate such external mask, maybe you could use mri_synthseg with the --robust flag and binarize the output? Cheers, /Eugenio
-- Juan Eugenio Iglesias http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Boa Sorte Silva, Narlon" narlon.silva@ubc.ca Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, January 30, 2023 at 01:14 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Skull stripping with external brainmask
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
External Email - Use Caution
Thanks Juan! It looks like the -xmask is available only for newer distributions of FreeSurfer. I’m using v7.1.1.
I appreciate the help though!
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 30, 2023, at 4:31 PM, Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu wrote:
[CAUTION: Non-UBC Email] Dear Narlon, I believe you can add -xmask [mask_volume_file] to your recon-all command. To generate such external mask, maybe you could use mri_synthseg with the --robust flag and binarize the output? Cheers, /Eugenio
-- Juan Eugenio Iglesias http://secure-web.cisco.com/1BmL6zZFY6WuwOU6V3ygO74VJ9eO2sbcTDHLY1JcQN81oMh_...http://secure-web.cisco.com/1BW06zkVyDqGypLPHvGJxaozoYyfDj2MCLIum4bZL_4KmeLs5wjyyZBlWBI3X9abX_rXjxLUtdAvLnehxBXS7uXZAUmU29qhecYfq7Zl_I0Pke4TkUbcD48kPg6E-_7rHle3mliGJKFq6P__rQIs1VnIVbcUrelyDZ5GeG1DtJv6v5fK6sDn-tifwjEuxvJyguhf3IWw3z7xZt4MdFFPcxKg1l2IkW4foIOFwPR57GaAAqc4fL-Db72HUgP8RBZIzq3GsfvFf9MvOQ6zrZO08NjMGs_fK-eNddjg5r31SCEdMJKIPAPT8KX7xOaG6nXPO/http%3A%2F%2Fwww.jeiglesias.com%2F
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Boa Sorte Silva, Narlon" <narlon.silva@ubc.camailto:narlon.silva@ubc.ca> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, January 30, 2023 at 01:14 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Skull stripping with external brainmask
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.camailto: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
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