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, 2014
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit 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
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