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
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