Error with running retinotopy glm - Freesurfer

21 Jul 2021


      Dear all,
Using FreeSurfer 7.1.1, I made my analysis file with the following (I assume -nksip should be in the number of TRs and not in seconds):
mkanalysis-sess -analysis retino_surf_pr_lh_sm0 -surface self lh -fwhm 0 -fsd bold -per-run -retinotopy 32 -spmhrf 0 -paradigm retino.par -TR .800 -nskip 10 -mcextreg -runlistfile retino_all_runs.txt
Then I ran the glm with the following:
selxavg3-sess -sf sessid_retino -df sessdir -analysis retino_surf_pr_lh_sm0
But I kept getting the following error message at the end of the log file:
-------------------------fast_selxavg3b.m 7.1.1————————————
outtop = /gpfs/milgram/scratch60/chun/yx55/mri-space/studies/localizers/unpackdata
Extension format = nii.gz
INFO: key nSliceGroups unrecognized, line 12, skipping
Excluding 10 points
nruns = 4
autostimdur = 
outanadir = /gpfs/milgram/scratch60/chun/yx55/mri-space/studies/localizers/unpackdata/20210719_localizer_10/bold/retino_surf_pr_lh_sm0
Excluding 10 points
Excluding 10 points
Excluding 10 points
Excluding 10 points
Found 125600/133962 (93.8) voxels in mask 1
Creating Design Matrix 
... creation time = 0.007 sec
DoMCFit = 1
ntptot = 1380, nX = 88, DOF = 1292
Saving X matrix to /gpfs/milgram/scratch60/chun/yx55/mri-space/studies/localizers/unpackdata/20210719_localizer_10/bold/retino_surf_pr_lh_sm0/Xtmp.mat
Error using svd
Input to SVD must not contain NaN or Inf.
Error in cond (line 35) 
s = svd(A);
Error in fast_selxavg3b (line 389) 
XCond = cond(XtX);
...
...
—————————————————————
ERROR: fast_selxavg3() failed\n
How should I fix this error? Any suggestions would be greatly appreciated. Thanks so much!
Best,
Yaoda Xu
External Email - Use Caution