External Email - Use Caution
Thanks Matt.
However I am wondering why the -expert flag is not working?
Regards,
Jerome
On Tue, 30 Dec 2025 at 11:23, freesurfer-request@nmr.mgh.harvard.edu wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- Problem using my own mask in recon-all (Jerome Maller)
- Re: Problem using my own mask in recon-all (Glasser, Matthew)
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 Message-ID: <CAMsE-JKS3KGXtTFGqGfU0ysnCwn-C8= ngZ5uf+3v-h-dZ4SHpA@mail.gmail.com> Content-Type: multipart/alternative; boundary="000000000000a7a85006472c69f9"
External Email - Use CautionHi 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