Hi IPL Neurosurgery
it seems that you have no read or write permission to the freesurfer tools.
/home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied.
you can change the permission with sudo chmod -R 777 freesurfer
Hope this helps Cheers Jürgen
----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland
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Am 11.03.2017 um 10:56 schrieb IPL Neurosurgery:
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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