hii doug Thank you so much.. :)
Regards Neha On Tue, Jan 12, 2016 at 10:02 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > 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/ > > > _______________________________________________ > 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. > >
_______________________________________________ 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.
