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 .datError 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 needed1/1 Sess01 002 lh ---------
Thu Jan 12 12:51:14 GMT 2012 Sess01 002 Update not neededThu 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, 2011Warning: 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 .datError 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@nmr.mgh.harvard.edu
-
Ivan Alvarez