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 <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>.
>>
>> >> >> >> >> >> >> >>
>> 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
>>
>
> --
> 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/
>
>
> _______________________________________________
> 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
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> but does not contain patient information, please contact the sender and
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>
>
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contains patient information, please contact the Partners Compliance HelpLine at
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