Hi Ivan, can you send me verbgen.sm5.lh/analysis.info? doug Ivan Alvarez wrote: > Dear Freesurfers, > > I recently attempted my first FSFAST analysis following the tutorial > on http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt > <http://nmr.mgh.harvard.edu/%7Egreve/fsfast.intro.ppt> while using my > own data. > > I stumbled across an error in selxavg3-sess which I can't decipher. > The problem seems to arise when running the Matlab script > fast_selxavg3.m andra returns: > > outtop = /media/data/analysis/FREESURFER_TEST/Project > > Extension format = nii.gz > > Error using basename > > Too many input arguments. > > > Error in fast_ldanaflac (line 423) > > nuisregevname = basename(nuisreg,'dat'); % remove .dat > > > Error in fast_selxavg3 (line 53) > > flac0 = fast_ldanaflac(analysis); > > > > I have looked through the Freesurfer documentation and mailing list > but couldn't spot anyone with this issue. I am attaching the full log > below, any insights would be greatly appreciated! > > > > > ivan@sirsa:/media/data/analysis/FREESURFER_TEST/Project$ > selxavg3-sess -sf sessid -analysis verbgen.sm5.lh > > Surface data fsaverage lh > > -------------------------------------------------------------- > > selxavg3-sess logfile is > /media/data/analysis/FREESURFER_TEST/Project/log/selxavg3-sess-bold-verbgen.sm5.lh-120112125113.log > > -------------------------------------------------------------- > > preproc-sess -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project > -a verbgen.sm5.lh -nolog > > -------------------------------------------------------------- > > preproc-sess logfile is /dev/null > > -------------------------------------------------------------- > > $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ > > ivan > > setenv FREESURFER_HOME /home/ivan/freesurfer > > setenv SUBJECTS_DIR /home/ivan/freesurfer/subjects > > Linux sirsa 2.6.35-31-generic #63-Ubuntu SMP Mon Nov 28 19:29:10 UTC > 2011 x86_64 GNU/Linux > > /media/data/analysis/FREESURFER_TEST/Project > > /home/ivan/freesurfer/fsfast/bin/preproc-sess > > -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -a > verbgen.sm5.lh -nolog > > Thu Jan 12 12:51:13 GMT 2012 > > instem f > > mc 1 f fmcpr > > stc 0 fmcpr > > sm 0 > > mask 1 brain > > Sess01 Template ----------------------------- > > mktemplate-sess -s Sess01 -d > /media/data/analysis/FREESURFER_TEST/Project -fsd bold -nolog -update > > > > Session: /media/data/analysis/FREESURFER_TEST/Project/Sess01 > ---------------- > > Thu Jan 12 12:51:13 GMT 2012 > > Detected input format at nii > > Sess01 Update not needed > > Run: 001 ---------------- > > Thu Jan 12 12:51:13 GMT 2012 > > Sess01 001 Update not needed > > Run: 002 ---------------- > > Thu Jan 12 12:51:13 GMT 2012 > > Sess01 002 Update not needed > > Thu Jan 12 12:51:13 GMT 2012 > > mktemplate-sess completed > > Sess01 Mask ------------------------ > > mkbrainmask-sess -maskstem brain -fsd bold -s Sess01 -d > /media/data/analysis/FREESURFER_TEST/Project -nolog -update > > ------------------------------------------------ > > /media/data/analysis/FREESURFER_TEST/Project/Sess01 > > Thu Jan 12 12:51:13 GMT 2012 > > Sess01 Update not needed for session-level mask > > Sess01 Update not needed for run 001 mask > > Sess01 Update not needed for run 001 meanval > > Sess01 Update not needed for run 002 mask > > Sess01 Update not needed for run 002 meanval > > Thu Jan 12 12:51:13 GMT 2012 > > mkbrainmask-sess done > > Sess01 Registration ----------------------------- > > register-sess -s Sess01 -d > /media/data/analysis/FREESURFER_TEST/Project -fsd bold -dof 6 -per-run > -nolog -update > > -------------------------------------------------------------- > > register-sess logfile is /dev/null > > -------------------------------------------------------------- > > Thu Jan 12 12:51:13 GMT 2012 > > > setenv SUBJECTS_DIR /home/ivan/freesurfer/subjects > > cd /media/data/analysis/FREESURFER_TEST/Project > > /home/ivan/freesurfer/fsfast/bin/register-sess -s Sess01 -d > /media/data/analysis/FREESURFER_TEST/Project -fsd bold -dof 6 -per-run > -nolog -update > > > freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > > Linux sirsa 2.6.35-31-generic #63-Ubuntu SMP Mon Nov 28 19:29:10 UTC > 2011 x86_64 GNU/Linux > > > > Session: /media/data/analysis/FREESURFER_TEST/Project/Sess01 > ---------------- > > Thu Jan 12 12:51:13 GMT 2012 > > Run: 001 ---------------- > > Thu Jan 12 12:51:14 GMT 2012 > > Update not needed > > Run: 002 ---------------- > > Thu Jan 12 12:51:14 GMT 2012 > > Update not needed > > Thu Jan 12 12:51:14 GMT 2012 > > register-sess completed > > Sess01 MC ----------------------------- > > mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d > /media/data/analysis/FREESURFER_TEST/Project -fsd bold -per-run -nolog > -update > > Logfile is /dev/null > > ------------------------------------------- > > /media/data/analysis/FREESURFER_TEST/Project/Sess01 > > RunList: 001 002 > > Sess01 001 Update not needed > > Sess01 002 Update not needed > > > Thu Jan 12 12:51:14 GMT 2012 > > mc-sess completed SUCCESSFULLY > > Sess01 To Surface ----------------------------- > > rawfunc2surf-sess -fwhm 5 -s Sess01 -d > /media/data/analysis/FREESURFER_TEST/Project -fsd bold -hemi lh -nolog > -update > > instem fmcpr > > outstem fmcpr.sm5.fsaverage.hemi > > ------------------------------ > > 1/1 Sess01 > > 1/1 Sess01 001 lh --------- > > Thu Jan 12 12:51:14 GMT 2012 > > Sess01 001 Update not needed > > 1/1 Sess01 002 lh --------- > > Thu Jan 12 12:51:14 GMT 2012 > > Sess01 002 Update not needed > > > Thu Jan 12 12:51:14 GMT 2012 > > rawfunc2surf-sess completed > > ---------------------------------------- > > Started at Thu Jan 12 12:51:13 GMT 2012 > > Ended at Thu Jan 12 12:51:14 GMT 2012 > > preproc-sess done > > ------------------------------------------- > > /media/data/analysis/FREESURFER_TEST/Project/Sess01 > > Thu Jan 12 12:51:14 GMT 2012 > > anadir = > /media/data/analysis/FREESURFER_TEST/Project/Sess01/bold/verbgen.sm5.lh > > DoGLMFit = 1 > > DoContrasts = 1 > > UpdateNeeded = 1 > > ------------------------------------------ > > ------- matlab output -------------------- > > Warning: Unable to open display 'iconic'. You will not be able to > display graphics on the screen. > > > < M A T L A B (R) > > > Copyright 1984-2011 The MathWorks, Inc. > > R2011b (7.13.0.564) 64-bit (glnxa64) > > August 13, 2011 > > > Warning: Duplicate directory name: /home/ivan/matlab. > > > > To get started, type one of these: helpwin, helpdesk, or demo. > > For product information, visit www.mathworks.com. > > > > >> >> >> >> >> >> >> /home/ivan/freesurfer/fsfast/toolbox/fast_selxavg3.m > > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > > #@# Sess01 ############################### > > /media/data/analysis/FREESURFER_TEST/Project/Sess01 > > ------------------------- > > $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ > > /home/ivan/freesurfer/fsfast/toolbox/fast_selxavg3.m > > /home/ivan/freesurfer/fsfast/toolbox/fast_ldanaflac.m > > /home/ivan/freesurfer/matlab/MRIread.m > > ------------------------- > > outtop = /media/data/analysis/FREESURFER_TEST/Project > > Extension format = nii.gz > > Error using basename > > Too many input arguments. > > > Error in fast_ldanaflac (line 423) > > nuisregevname = basename(nuisreg,'dat'); % remove .dat > > > Error in fast_selxavg3 (line 53) > > flac0 = fast_ldanaflac(analysis); > > > > >> ------------------------------------------ > > ERROR: fast_selxavg3() failed\n > > > -- > Kind Regards, > Ivan Alvarez > > PhD Student > Imaging and Biophysics Unit > UCL Institute of Child Health > 30 Guildford Street, London, WC1N 1EH > ------------------------------------------------------------------------ > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
