Re: [Freesurfer] trac-all -prep error

2021-12-21 Thread Salar Dini, Elaheh
External Email - Use Caution Hello, I've just realized that one of our fellow freesurfer user, Jürgen, has faced the same problem which was originating from the file "dwi_orig_las.1.bvals“ was renamed to „dwi_orig_las.bvals“ . Based on Dr. Yendiki's direction is specific to th

Re: [Freesurfer] trac-all -prep error

2021-12-21 Thread Salar Dini, Elaheh
External Email - Use Caution Dear Anastasia, I just wanted to follow-up on my previous message with having this in mind: the index.txt file should be a line of twenty-six 1, i.e. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1, in our case. For some reason, Freesurfer or FSL ca

Re: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter

2021-12-21 Thread Fischl, Bruce
External Email - Use Caution Hi Jee Won Can you send us the recon-all.log file? And ideally an example orig.mgz that we can try things on Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Kang, Jee Won Sent: Tuesday, December 21, 2021 9:19 AM To: freesurf