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 a OneDrive 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

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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.

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