Sorry, I've attached a matlab script. Copy it to $FREESURFER_HOME/matlab
and try again
doug
On 01/12/2016 09:59 AM, neha hooda wrote:
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
<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
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
<gr...@nmr.mgh.harvard.edu <mailto:gr...@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> <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
<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto: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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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/
function tmppath = fsgettmppath(tmppathdefault)
% tmppath = fsgettmppath(<tmppathdefault>)
% Gets path to a temporary folder (does NOT generate a random file name)
% First looks in the following order:
% 1. $TMPDIR - env var must exist and folder must exist
% 2. $TEMPDIR - env var must exist and folder must exist
% 3. /scratch - folder must exist
% 4. /tmp - folder must exist
% 5. tmppathdefault - if passed
% 6. current folder, ie, ./ (prints warning)
tmppath = getenv('TMPDIR');
if(~isempty(tmppath))
if(exist(tmppath))
return;
end
end
tmppath = getenv('TEMPDIR');
if(~isempty(tmppath))
if(exist(tmppath))
return;
end
end
tmppath = '/scratch';
if(exist(tmppath)) return; end
tmppath = '/tmp';
if(exist(tmppath)) return; end
if(nargin > 0)
tmppath = tmppathdefault;
if(exist(tmppath)) return; end
end
tmppath = './';
fprintf(['WARNING: fsgettmppath: could not find a temporary folder,' ...
' using current folder\n']);
return;
_______________________________________________
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.
