Hi Anup
I suspect the problem is choosing a subject with ".mgz" in the ID. I wouldn't include any of ".nii" ".mgz" or ".mgh" in a subject ID. Try rerunning and just using fsMM
cheers Bruce
On Wed, 14 Jun 2017, Anup Bidesi wrote:
Hello FreeSurfer Users,
New to Freesurfer, I'm attempting to recon-all using :
recon-all -all -i T1.nii -s op.nii.mgz (Attached recon-all log)
The automated process begins normally and seems to run Autorecon Prrocessing Stages 1-25, but at step 26 (I think) and then exits with Error, per log as seen below:
mghRead(/home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.th ickness, -1): could not open file. Filename extension must be .mgh, .mgh.gz or .mgz
Within the subject .mgz folder in Surf there was a tmp.pctsurfcon.14807 fold er with a file named lh.wm.mgh (size 569 kb).
I ran this process a couple of times and the autorecon process would exit at same step.I tried looking up the Archive for any similar previous error messages but did not find any. Please advise.
- FreeSurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Platform: Ubuntu 14.04
uname -a: Linux brainmindengineer-Precision-Tower-7910 3.13.0-117-generic
#164-Ubuntu SMP Fri Apr 7 11:05:26 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
- recon-all.log: see attached
Thanks for your help,
Anup