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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.



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