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. 
<jiglesiasgonza...@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_YnyGq6LFlCAYThBSAii6PDY-crsby327DNmE4TRPnqc1yddX1yT3iT4VJBH0SHefdlUn2RIP88pmMw9hqypXqGDwJG9_eiZn-UAxaTE45FwvaedJez0KD3aCDl5drqqOQphDsxjfyaaAkfwDJdEQucW_Z5EsRxUx1NWAg4fI039SSBj0Q1CsTjSwvwel6iruxOcIJZj62Ay17tprQPXIsvv7pheLROsBwDqqA3lzQIcy6MaYN9wazZxdXcDNm96dvH2DglxZl9qelMt7h/http%3A%2F%2Fwww.jeiglesias.com<http://secure-web.cisco.com/1BW06zkVyDqGypLPHvGJxaozoYyfDj2MCLIum4bZL_4KmeLs5wjyyZBlWBI3X9abX_rXjxLUtdAvLnehxBXS7uXZAUmU29qhecYfq7Zl_I0Pke4TkUbcD48kPg6E-_7rHle3mliGJKFq6P__rQIs1VnIVbcUrelyDZ5GeG1DtJv6v5fK6sDn-tifwjEuxvJyguhf3IWw3z7xZt4MdFFPcxKg1l2IkW4foIOFwPR57GaAAqc4fL-Db72HUgP8RBZIzq3GsfvFf9MvOQ6zrZO08NjMGs_fK-eNddjg5r31SCEdMJKIPAPT8KX7xOaG6nXPO/http%3A%2F%2Fwww.jeiglesias.com%2F>

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Boa Sorte Silva, Narlon" 
<narlon.si...@ubc.ca<mailto:narlon.si...@ubc.ca>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, January 30, 2023 at 01:14
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto: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.si...@ubc.ca<mailto: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


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