External Email - Use Caution Dear Freesurfer team,
I'm new to fMRI analysis and want to analyse Retinotopy data. I was following a
retinotopy analysis tutorial
(sites.psych.ualberta.ca/kylemathewson/retinotopy-in-freesurfercnl-protocol/#FUNC)
when I encountered a problem while running selx3avg-sess. I found that some
other people had similar issues on the mailing list, but most often the reason
was that there were only positive polar or eccen runs. In this case, I'm
analyzing all 4 conditions ( eccen/pos; eccen/neg; polar/pos; polar/neg) in 4
separate runs. The TR is 2 seconds and there are 32 acquisitions per run.
I'm running the following freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
These are the first steps of the analysis, which ran without an error:
1. preproc-sess -s T1_EarlyVisualLesion -surface self lhrh -fsd Retinotopy
-mni305 -fwhm 5 -per-run
2. mkanalysis-sess -a Retinotopy.T1_EarlyVisualLesion.lh -surface self lh -TR 2
-retinotopy 64 -paradigm rtopy.par -fsd Retinotopy -fwhm 5 -per-run
When running the following:
selxavg3-sess -a Retinotopy.T1_EarlyVisualLesion.lh -s T1_EarlyVisualLesion
the following error appers:
% /data/local/Software/freesurfer/subjects
% Retinotopy.T1_EarlyVisualLesion.lh
which fast_selxavg3
which fast_ldanaflac
which MRIread
fast_selxavg3b('/data/local/Software/freesurfer/subjects/T1_EarlyVisualLesion/Retinotopy/Retinotopy.T1_EarlyVisualLesion.lh/sxa3.config.txt')
if(~fast_fileexists('/tmp/selxavg3-sess-9836.ok')); quit; end
%--------------------------------
quit;
------------------------------------------
------------------------------------------
------- matlab output --------------------
MATLAB is selecting SOFTWARE OPENGL rendering.
< M A T L A B (R) >
Copyright 1984-2019 The MathWorks, Inc.
R2019a (9.6.0.1072779) 64-bit (glnxa64)
March 8, 2019
To get started, type doc.
For product information, visit
http://secure-web.cisco.com/1vaPLvSV7ygYtI5_OZ6fwnXZPrdpCQWbuMTl3qMCoMm4YYMnGcCb6Nfuh4HA92xXGYMTq1-3Cku0d41CtFPaPfes1skYbD_89DOOleKjHQYkHb3hzqfB8Y3uTHLrvfbiW7QwVe63tDlKsTCNtsoRB_aGdsisuvy3Lv0jRcGd62tGe_ze4btABZAYsXrtWMZ2nBcJnOVXzlRlvPtA4sH2EHTCo0TqqiK13o0oxKMgVT6QLC2MDUUuojjchLlcsSZAVBNraatVB8YZiGi5UCmKDiA/http%3A%2F%2Fwww.mathworks.com.
>> >> >> >> /data/local/Software/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> /data/local/Software/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>> /data/local/Software/freesurfer/matlab/MRIread.m
>> >> >> starting fast_selxavg3b
#@# T1_EarlyVisualLesion ###############################
/data/local/Software/freesurfer/subjects/T1_EarlyVisualLesion
-------------------------
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-------------------------
outtop = /data/local/Software/freesurfer/subjects
Extension format = nii.gz
INFO: key nSliceGroups unrecognized, line 11, skipping
nruns = 4
autostimdur =
outanadir =
/data/local/Software/freesurfer/subjects/T1_EarlyVisualLesion/Retinotopy/Retinotopy.T1_EarlyVisualLesion.lh
Found 44756/124286 (36.0) voxels in mask 1
Creating Design Matrix
... creation time = 0.005 sec
DoMCFit = 1
ntptot = 128, nX = 36, DOF = 92
Saving X matrix to
/data/local/Software/freesurfer/subjects/T1_EarlyVisualLesion/Retinotopy/Retinotopy.T1_EarlyVisualLesion.lh/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 394)
XCond = cond(XtX);
>> ------------------------------------------
ERROR: fast_selxavg3() failed\n
I attached the xmap file and noticed that there are 4 rows/columns that are all
'Nan' ( 5,6, 17 and 18).
I'm not sure why nX is 36: because freesurfer found 44756/124286 (36.0) voxels
or because it should be the amount of TR's during the run (32 conditions of 2
seconds each)?
The size of each run (.nii) is (112 by 112 by 54 by 32). So if nX should
contain the amount of TR's per run, I'm not sure why it's adding 4 columns/rows
to nX.
Any help and advice to fix this problem is very much appreciated.
Thanks in advance,
Michael Vanhoyland
Department of Neurophysiology
KULeuven, Belgium
Xtmp.mat
Description: Xtmp.mat
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