hii doug

Thanks for the reply. But it gives the error.

------------------------------------------
------- 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
Undefined function or variable 'fsgettmppath'.

Error in load_nifti (line 67)
new_niftifile = sprintf('%s.load_nifti.m.nii', tempname(fsgettmppath));

Error in MRIread (line 158)
hdr = load_nifti(fspec,headeronly);

Error in flac_customize (line 87)
mri = MRIread(fstem,1);

Error in fast_selxavg3 (line 65)
flac0 = flac_customize(flac0);

>> ------------------------------------------
ERROR: fast_selxavg3() failed\n

On Mon, Jan 11, 2016 at 9:37 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

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, 2014

To 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

_______________________________________________
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
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