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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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From: IPL Neurosurgery
Sent: 11 March 2017 15:26:30
To: freesurfer@nmr.mgh.harvard.edu
Subject: Error while attempting Segmentation
 

Hi,


We have newly installed Freesurfer. We are a novice. We were trying to segment our data set. We used the following command. We attached the log.


Command: recon-all -s testsample -all

Output:

[iplneurosurgery@localhost /]$ recon-all -s testsample -all
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /home/iplneurosurgery/Documents/freesurfer/subjects
Actual FREESURFER_HOME /home/iplneurosurgery/Documents/freesurfer
-rw-rw-r--. 1 iplneurosurgery iplneurosurgery 18906 Mar 11 12:15 /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/scripts/recon-all.log
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
/home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied.
'/usr/local/freesurfer/bin/recon-all' -> '/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/scripts/recon-all.local-copy'
#--------------------------------------------
#@# MotionCor Sat Mar 11 14:48:00 IST 2017
Found 1 runs
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz

/home/iplneurosurgery/Documents/freesurfer/subjects/testsample

 mri_convert /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz --conform

mri_convert.bin /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz...
TR=483.49, TE=12.00, TI=0.00, flip angle=73.00
i_ras = (-0.989525, -0.140773, -0.0319737)
j_ras = (0.144349, -0.962296, -0.230541)
k_ras = (0.00168578, -0.232741, 0.972537)
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz...

 mri_add_xform_to_header -c /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/transforms/talairach.xfm /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Mar 11 14:48:05 IST 2017
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri

 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50

/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
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
Sat Mar 11 14:48:05 IST 2017
/home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied.
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.10571
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10571/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10571/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=483.49, TE=12.00, TI=0.00, flip angle=73.00
i_ras = (-1, 9.77889e-09, 1.16415e-09)
j_ras = (5.82077e-09, 0, -1)
k_ras = (1.21945e-08, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.10571/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Mar 11 14:48:07 IST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.10571/nu0.mnc ./tmp.mri_nu_correct.mni.10571/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10571/0/ -iterations 1000 -distance 50
/home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied.
ERROR: nu_correct
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 testsample exited with ERRORS at Sat Mar 11 14:48:07 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


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