Hi Falk
Thanks so much for your reply.
I checked the brainmask.mgz file and I guess it looks ok. I copied the screenshot below:
I appreciate if you have any comment on that.
Thanks a lot
Mona
[cid:17ab68b4-1c80-4094-b54b-b550ea25c630]
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
________________________________ From: falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.de Sent: Wednesday, August 21, 2019 5:42:54 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Nasiriavanaki, Zahra ZNASIRIAVANAKI@mgh.harvard.edu Subject: AW: [Freesurfer] recon_all hires
External Email - Use Caution
Hi Mona,
Potentially you have a bad skull strip resulting in a huge defect which will take a long time to correct. Simply fix your skull strip and you should be fine.
Best,
Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Nasiriavanaki, Zahra Gesendet: Dienstag, 20. August 2019 16:19 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] recon_all hires
Dear Freesurfer experts
I am doing recon-all on one of my subjects and it seems that it's stuck for days and not going through. I even re-run it and it's still stuck at the same spot as before.
I attached the log file and here is my command:
recon-all -all -s $subj -i /$subj/anat/$run/mT1v2.nii -expert expertopts/expert.opts -hires -mail zn025 -parallel
I appreciate any help.
Thanks
Mona
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
