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
Sent from Outlookhttp://aka.ms/weboutlook
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
0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number)
j.haenggi@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. -----------------------------------------------------------------------------------------------------
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
Sent from Outlook <recon-all.log>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
IPL Neurosurgery has shared a OneDrive file with you. To view it, click the link below.
https://1drv.ms/u/s!AiMzXSfGawBBdahGfvQrL5SwJT4 [https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]https://1drv.ms/u/s!AiMzXSfGawBBdahGfvQrL5SwJT4
recon-all.loghttps://1drv.ms/u/s!AiMzXSfGawBBdahGfvQrL5SwJT4
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.
Sent from Outlookhttp://aka.ms/weboutlook
________________________________ 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
Sent from Outlookhttp://aka.ms/weboutlook
freesurfer@nmr.mgh.harvard.edu
-
IPL Neurosurgery -
Juergen Haenggi