[Freesurfer] mri_watershed and improvements of skullstripping

2023-07-30 Thread Michelangelo Fabbrizzi
External Email - Use Caution Dear Freesurfer experts, I am new to FS, and I would have couple of questions. I used in sequence: A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1 B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon C- recon-all -skullstri

Re: [Freesurfer] mri_watershed and improvements of skullstripping

2023-07-30 Thread Michelangelo Fabbrizzi
External Email - Use Caution Dear All, another question: after the below if I use the command to run autorecon2: recon-all -s sub-01_recon -autorecon2 I get the following error: ERROR: cannot find or read transforms/talairach.m3z Can you help me please? Thanks, regards, Michel

[Freesurfer] Command not found

2023-07-30 Thread Rachel Wagner
External Email - Use Caution Hello all, I have not used freesurfer in a couple of months, and have returned to create a new cortical projection image. I’m having an issue with my commands, they don’t seem to be recognized anymore and I’m not sure why: developer@developer-Virtua