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Today's Topics:
1. Problem using my own mask in recon-all (Jerome Maller)
2. Re: Problem using my own mask in recon-all (Glasser, Matthew)
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Message: 1
Date: Tue, 30 Dec 2025 08:45:24 -0600
From: Jerome Maller <jerome.maller@monash.edu>
Subject: [Freesurfer] Problem using my own mask in recon-all
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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Hi Freesurfer experts.
I am trying to process a T1-MPRAGE 7T scan with 0.5mm isotropic resolution
with the recon-all -highres flag. FS is struggling to make a good mask even
though I’ve tried various combinations in the recon-all command (e.g.
different -skullstrip -wsthresh numbers, -wsmore, different -watershed
atlases). I have tried with and without neck removal (using FSL’s
robustfov) as well as bias field correction (via SPM and also FSL’s FAST),
and feeding in with and without the scan already brain extracted (via
robex). I am now trying to feed in my pre-made mask using the -expert flag.
* I have named my pre-made mask as brainmask.mgz and placed it in the
directory where my t1.nii.gz is located
* I have made a text file (called expert.opts) that contains:
mri_mask brainmask.mgz
My recon-all command calls the file using -expert expert.opts
However, recon-all seems to ignore the calling of the expert.opts and so
tries to make its own mask…
So my question is: am I correctly using the =expert flag and expert.opts to
use my pre-made brainmask.mgz?
PS. I am using FS version 7.1 (as I am running Ubuntu 18.04 and can’t
upgrade due to lots of other software running on the computer)
Thankyou!
Jerome
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Message: 2
Date: Tue, 30 Dec 2025 17:23:25 +0000
From: "Glasser, Matthew" <glasserm@wustl.edu>
Subject: [Freesurfer] Re: Problem using my own mask in recon-all
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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You could try running the data through the HCP Pipelines, which assist FreeSurfer in making a good brain extraction.
You would want to make a copy of the templates at 0.5mm resolution instead of the 0.7mm resolution to ensure the full resolution of your scan is used.
Matt.
From: Jerome Maller <jerome.maller@monash.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, December 30, 2025 at 8:45 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Problem using my own mask in recon-all
External Email - Use Caution
Hi Freesurfer experts.
I am trying to process a T1-MPRAGE 7T scan with 0.5mm isotropic resolution with the recon-all -highres flag. FS is struggling to make a good mask even though I’ve tried various combinations in the recon-all command (e.g. different -skullstrip -wsthresh numbers, -wsmore, different -watershed atlases). I have tried with and without neck removal (using FSL’s robustfov) as well as bias field correction (via SPM and also FSL’s FAST), and feeding in with and without the scan already brain extracted (via robex). I am now trying to feed in my pre-made mask using the -expert flag.
* I have named my pre-made mask as brainmask.mgz and placed it in the directory where my t1.nii.gz is located
* I have made a text file (called expert.opts) that contains:
mri_mask brainmask.mgz
My recon-all command calls the file using -expert expert.opts
However, recon-all seems to ignore the calling of the expert.opts and so tries to make its own mask…
So my question is: am I correctly using the =expert flag and expert.opts to use my pre-made brainmask.mgz?
PS. I am using FS version 7.1 (as I am running Ubuntu 18.04 and can’t upgrade due to lots of other software running on the computer)
Thankyou!
Jerome
--
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