I was trying to do retinotopic analysis on a dataset using the new Freesurfer v5.0.0 on a 64bit Linux (Red Hat 4.1.2-48 CentOS 5.5) computer and have run across a problem.

I set up the analysis using mkanalysis-sess as suggested in an earlier email to the list, but when I try to run selxavg3-sess it errors out.

The commands I ran were:
mkanalysis-sess -analysis retino26-lh -surface self lh -fwhm 0 -retinotopy 55.467 -paradigm retino.par -TR 2.6 -runlistfile polar_runs.txt
selxavg3-sess -a retino26-lh -s spicyrobin -df retino-dirfile

It gets through all the preprocessing and then this is the output (the matlab error is one I know about, if that is causing the problem I can talk to our IT here about getting it fixed):

preproc-sess done
-------------------------------------------
/home/kcb/mri-space/spicyrobin
Tue Aug 31 15:29:38 EDT 2010
anadir = /home/kcb/mri-space/spicyrobin/bold/retino26-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 1984-2010 The MathWorks, Inc.
                Version 7.10.0.499 (R2010a) 64-bit (glnxa64)
                              February 5, 2010

To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

Warning: Executing startup failed in matlabrc.
This indicates a potentially serious problem in your MATLAB setup,
which should be resolved as soon as possible. Error detected was:
MATLAB:TooManyInputs
Too many input arguments.
> In matlabrc at 227
>> >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.88.2.2 2010/07/16 15:31:24 greve Exp $
outtop = /home/kcb/mri-space
Extension format = nii
nruns = 4
autostimdur =

outanadir = /home/kcb/mri-space/spicyrobin/bold/retino26-lh
Found 117359/125110 (93.8) voxels in mask
Creating Design Matrix
... creation time = 0.008 sec
DoMCFit = 1
ntptot = 1024, nX = 36, DOF = 988
Saving X matrix to /home/kcb/mri-space/spicyrobin/bold/retino26-lh/Xtmp.mat
??? Error using ==> svd
Input to SVD must not contain NaN or Inf.

Error in ==> cond at 40
   s = svd(A);

Error in ==> fast_selxavg3 at 247
XCond = cond(XtX);

>> ------------------------------------------
ERROR: fast_selxavg3() failed\n

thanks,

Katie