Hello Doug, Ah! this was the root of the problem. A conflict was generated with the Stanford Vistasoft toolbox, which also contains a 'basename.m' file. Once removed from the Matlab path list, selxavg3-sess behaves normally.
Thank you for the help! Kind Regards, Ivan Alvarez PhD Student Imaging and Biophysics Unit UCL Institute of Child Health 30 Guildford Street, London, WC1N 1EH On 17/01/12 17:48, Douglas N Greve wrote: > Hi Ivan, I can't pin down what the problem is. This is very strange. > There are a couple of things that you can try. First, start matlab and > run the command > which basename > This should return /home/ivan/freesurfer/fsfast/toolbox/basename.m > If it returns something else or multiple functions, then this is the > problem. > > doug > > > Ivan Alvarez wrote: >> Hello Doug, >> >> Please find attached the verbgen.sm5.lh/analysis.info file. >> >> Kind Regards, >> Ivan Alvarez >> >> PhD Student >> Imaging and Biophysics Unit >> UCL Institute of Child Health >> 30 Guildford Street, London, WC1N 1EH >> >> >> On 13/01/12 19:20, Douglas N Greve wrote: >>> 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 >>> > _______________________________________________ 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. 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