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