Hi,
It looks like Freesurfer can't read bert's brainmask.mgz volume. Can you
ls -l bert's mri directory and see if that file is there and you have
proper permission to read it? mri_watershed is looking for that file
because the command says to keep the edits from brainmask.mgz, but that
file is normally generated after the watershed step that is failing and
I don't see any previous instances of recon-all in the log file where
brainmask.mgz was created.
Best,
Allison
On 03/20/2017 02:05 AM, IPL Neurosurgery wrote:
IPL Neurosurgery has shared a OneDrive file with you. To view it,
click the link below.
<https://1drv.ms/u/s%21AiMzXSfGawBBdqVKAa4rOGRiPGw>
recon-all 1.log <https://1drv.ms/u/s%21AiMzXSfGawBBdqVKAa4rOGRiPGw>
[recon-all 1.log]
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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