Thats odd. Does that file exist? What are the permissions of it?
ls -l /home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz
IPL Neurosurgery has shared aâ¯OneDriveâ¯file with you. To view it, click the link below.
https://1drv.ms/u/s!AiMzXSfGawBBdqVKAa4rOGRiPGw [https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]https://1drv.ms/u/s!AiMzXSfGawBBdqVKAa4rOGRiPGw
recon-all 1.loghttps://1drv.ms/u/s!AiMzXSfGawBBdqVKAa4rOGRiPGw
Hi,
We have encountered a error in skull stripping process in bert sample. We are a novice. We attached the log.
Command : recon-all -s bert -all
#@# Skull Stripping Sat Mar 18 14:58:05 IST 2017 /home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri
mri_watershed -rusage /home/iplneurosurgery/Documents/freesurfer/subjects/bert/touch/rusage.mri_watershed.dat -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /home/iplneurosurgery/Documents/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) mghRead(/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz, -1): read error
The input file is T1.mgz The output file is brainmask.auto.mgz No such file or directory Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s bert exited with ERRORS at Sat Mar 18 14:58:06 IST 2017
freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Platform: Cent OS 7
uname -a : 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Any Suggestion will be appreciated.
Thanking you,
IPL Neurosurgery.
Sent from Outlookhttp://aka.ms/weboutlook _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer