Re: [Freesurfer] Help (Freeview fails to launch)

2023-12-28 Thread fsbuild
External Email - Use Caution That message could be the result of missing system libraries which the Ubuntu 22 FS 7.4.1 .deb package will try to automatically identify, download and install for you. You can download the package via the

Re: [Freesurfer] Recon-all failing with pre-skullstripped input data (mri_em_register can't find brainmask.mgz)

2023-12-28 Thread Huang, Yujing
This is from Freesurfer wiki - https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ Q. I have already skull-stripped data. Can I submit it to recon-all? A: If your skull-stripped volume does not have the cerebellum, then no. If it does, then yes, however you will have to run the data

[Freesurfer] Recon-all failing with pre-skullstripped input data (mri_em_register can't find brainmask.mgz)

2023-12-28 Thread James Hengenius
External Email - Use Caution Hello FS experts, I downloaded some anatomical data. I have defaced full images and pre-skullstripped images for each participant. I tried the defaced images first, but FS skullstripping looks a little off (possibly because the defacing hides bits of

Re: [Freesurfer] Brainstem segmentation without pre-processing

2023-12-28 Thread Iglesias Gonzalez, Juan E.
Dear Ali, Making a SynthSeg version of the tool is on the to-do list but has not happened yet. For now, you need to run recon-all. The good news is that you get a ton of additional useful information on the brains! Kind regards, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: