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.
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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