Hi Neha, I've attached a file called load_nifti.m. Put this in $FREESURFER_HOME/matlab (after making a backup of what is there). Then re-run and let me know if that fixes the problem. doug
On 01/09/2016 06:00 AM, neha hooda wrote:
Hii
I am using freesurfer to find the resting state connectivity. I used selxavg3-sess to analyze the data. But it neither terminates nor gives the error. Any help will be appreciated.
Regards Neha
selxavg3-sess logfile is /home/neha/projectfolder/log/selxavg3-sess-bold-fc.lpccseed.surf.lh-160109152215.log
preproc-sess -s sessionid -d /home/neha/projectfolder -a fc.lpccseed.surf.lh -nolog
preproc-sess logfile is /dev/null
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ NC_2 setenv FREESURFER_HOME /home/NC_2/shubham/freesurfer/freesurfer/ setenv SUBJECTS_DIR /home/neha/AKE01/PA0/ST0/ Linux tapan 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux /home/neha/projectfolder /home/NC_2/shubham/freesurfer/freesurfer//fsfast/bin/preproc-sess -s sessionid -d /home/neha/projectfolder -a fc.lpccseed.surf.lh -nolog Sat Jan 9 15:22:16 IST 2016 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain sessionid Template ----------------------------- mktemplate-sess -s sessionid -d /home/neha/projectfolder -fsd bold -nolog -update
Session: /home/neha/projectfolder/sessionid ---------------- Sat Jan 9 15:22:16 IST 2016 Detected input format at nii.gz sessionid Update not needed Run: 004 ---------------- Sat Jan 9 15:22:16 IST 2016 sessionid 004 Update not needed Sat Jan 9 15:22:16 IST 2016 mktemplate-sess completed sessionid Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s sessionid -d /home/neha/projectfolder -nolog -update
/home/neha/projectfolder/sessionid Sat Jan 9 15:22:16 IST 2016 sessionid Update not needed for session-level mask sessionid Update not needed for run 004 mask sessionid Update not needed for run 004 meanval Sat Jan 9 15:22:16 IST 2016 mkbrainmask-sess done sessionid Registration ----------------------------- register-sess -s sessionid -d /home/neha/projectfolder -fsd bold -dof 6 -per-run -nolog -update
register-sess logfile is /dev/null
Sat Jan 9 15:22:16 IST 2016
setenv SUBJECTS_DIR /home/neha/AKE01/PA0/ST0/ cd /home/neha/projectfolder /home/NC_2/shubham/freesurfer/freesurfer//fsfast/bin/register-sess -s sessionid -d /home/neha/projectfolder -fsd bold -dof 6 -per-run -nolog -update
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux tapan 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
Session: /home/neha/projectfolder/sessionid ---------------- Sat Jan 9 15:22:16 IST 2016 Run: 004 ---------------- Sat Jan 9 15:22:16 IST 2016 Update not needed Sat Jan 9 15:22:16 IST 2016 register-sess completed sessionid MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s sessionid -d /home/neha/projectfolder -fsd bold -per-run -nolog -update Logfile is /dev/null
/home/neha/projectfolder/sessionid RunList: 004 sessionid 004 Update not needed
Sat Jan 9 15:22:16 IST 2016 mc-sess completed SUCCESSFULLY sessionid To MNI305 ----------------------------- rawfunc2tal-sess -fwhm 5 -s sessionid -d /home/neha/projectfolder -fsd bold -nolog -update -subcort-mask -per-run
1/1 sessionid 1/1 sessionid 004 ---------------- Sat Jan 9 15:22:16 IST 2016 /home/neha/projectfolder/sessionid/bold/004/masks/brain.mni305.2mm.nii.gz does not need updating sessionid 004 Update not needed
Sat Jan 9 15:22:16 IST 2016 rawfunc2tal-sess completed
Started at Sat Jan 9 15:22:16 IST 2016 Ended at Sat Jan 9 15:22:16 IST 2016 preproc-sess done
/home/neha/projectfolder/sessionid Sat Jan 9 15:22:17 IST 2016 anadir = /home/neha/projectfolder/sessionid/bold/fc.lpccseed.surf.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1
------- matlab output -------------------- MATLAB is selecting SOFTWARE OPENGL rendering.
< M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014b (8.4.0.150421) 64-bit (glnxa64) September 15, 2014To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com http://www.mathworks.com.
> >> >> >> >>
sxa3pwd =
/home/neha/projectfolder
sxa3cmd =
/home/NC_2/shubham/freesurfer/freesurfer//fsfast/bin/selxavg3-sess -s sessionid -a fc.lpccseed.surf.lh
/home/NC_2/shubham/freesurfer/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
#@# sessionid ############################### /home/neha/projectfolder/sessionid
$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /home/NC_2/shubham/freesurfer/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/NC_2/shubham/freesurfer/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/NC_2/shubham/freesurfer/freesurfer/matlab/MRIread.m
outtop = /home/neha/projectfolder Extension format = nii.gz rm: remove regular file `/tmp/tmp9865807.nii'? 0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer