External Email - Use Caution Dear Freesurfer experts,
To follow up on my previous email, I also tried the same code on a
different PC with Ubuntu 22.02.4 LTS and FreeSurfer version 7.4
This time, I also get an error at the stage of running selxavg3-sess:
"
/home/tonglab/Documents/Loic/retinotopy/sub-F019_sourceData/sess01
-------------------------
fast_selxavg3b.m 7.4.0
-------------------------
outtop = /home/tonglab/Documents/Loic/retinotopy/sub-F019_sourceData
Extension format = nii.gz
INFO: key nSliceGroups unrecognized, line 11, skipping
nruns = 3
autostimdur =
outanadir =
/home/tonglab/Documents/Loic/retinotopy/sub-F019_sourceData/sess01/bold/retinotopy.F019.02.lh/pr001
Found 429871/518993 (82.8) voxels in mask 1
Creating Design Matrix
... creation time = 0.003 sec
DoMCFit = 1
ntptot = 150, nX = 27, DOF = 123
Saving X matrix to
/home/tonglab/Documents/Loic/retinotopy/sub-F019_sourceData/sess01/bold/retinotopy.F019.02.lh/pr001/Xtmp.mat
XCond = NaN (normalized)
Warning: Matrix is singular to working precision.
> In fast_selxavg3b (line 403)
In sxa3 (line 9)
In run (line 91)
Computing contrast matrices
Warning: Matrix is singular to working precision.
> In fast_selxavg3b (line 441)
In sxa3 (line 9)
In run (line 91)
Warning: Matrix is singular to working precision.
> In fast_selxavg3b (line 441)
In sxa3 (line 9)
In run (line 91)
OLS Beta Pass
run 1 t= 0.0
reading data ... 2.94087
Global Mean 18794.10
Global In-Mask Mean = 18794.1 (NaN)
Rescale Target = 100
RescaleFactor = 0.00532082
OLS Residual Pass
run 1 t= 0.0
reading data ... 2.83474
Saving rho1
Found 0 voxels with corrected AR1 > 0.90
Not Whitening
Warning: Matrix is singular to working precision.
> In fast_glmfit (line 54)
In fast_selxavg3b (line 999)
In sxa3 (line 9)
In run (line 91)
Found 89122 zero-valued voxels
Computing contrasts
Starting contrasts
eccen J=2 -------------
Warning: Matrix is singular to working precision.
> In fast_fratiow (line 86)
In fast_selxavg3b (line 1161)
In sxa3 (line 9)
In run (line 91)
Warning: Matrix is singular, close to singular or badly scaled. Results may
be inaccurate. RCOND = NaN.
> In fast_fratiow (line 86)
In fast_selxavg3b (line 1161)
In sxa3 (line 9)
In run (line 91)
Error using betainc
X must be in the interval [0,1].
Error in FTest (line 51)
p = betainc(z, dof2/2, dof1/2);
Error in fast_selxavg3b (line 1163)
pmat = FTest(dof1, dof2, Fmat);
Error in sxa3 (line 9)
fast_selxavg3b('/home/tonglab/Documents/Loic/retinotopy/sub-F019_sourceData/sess01/bold/retinotopy.F019.02.lh/sxa3.config.txt')
Error in run (line 91)
evalin('caller', strcat(script, ';'));
"
This is the code I use for this stage:
"
polarRuns=(1 2 3)
#Polar
for((i=1; i<${#polarRuns[@]}+1; i++)); do
parName=$(printf run"%02d"_parad.par $i)
unset Num1 ;
unset Num2;
Num1=${polarRuns[i]} ; printf -v Num1 "%02d" $Num1 ;
#parName=run"$Num1"_parad.par;
printf -v Num2 "%03d" $Num1 ;
mkanalysis-sess -analysis retinotopy.F019.$Num1.lh -surface sub-F019 lh -TR
2 -retinotopy 32 -paradigm $parName -per-run -fsd bold -fwhm 5 -force; #
selxavg3-sess -a retinotopy.F019.$Num1.lh -s sess01 -per-run -monly sxa3.m;
/home/tonglab/MATLAB/R2023a/bin/matlab -nojvm -nodesktop -r "run
/home/tonglab/Documents/Loic/retinotopy/${SUB}_sourceData/sxa3.m";
done
"
Please see attached the annalysis info file of one of the runs (though the
error applies to all the runs)
Any advice would be highly appreciated at this stage.
Thanks,
Best,
-Loic
Le jeu. 1 juin 2023 à 11:00, Loïc Daumail <loic.daum...@gmail.com> a écrit :
> Dear FreeSurfer experts,
>
> I am trying to perform a retinotopy analysis using fs-fast with Freesurfer
> version 7.3.2 on a Mac OS Monterey Version 12.6.2
>
> Here is the error I am having (I saw this same error in the archive, but I
> wasn't able to find any solution email that followed regarding this issue):
>
> Saving X matrix to
> /Users/tong_processor/Desktop/Loic/retinotopy/old_Hojin_mri_data/F094_fsfast/sess01/bold/retinotopy.F094.07.lh/pr007/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 in sxa3 (line 9)
>
> fast_selxavg3b('/Users/tong_processor/Desktop/Loic/retinotopy/old_Hojin_mri_data/F094_fsfast/sess01/bold/retinotopy.F094.07.lh/sxa3.config.txt')Error
> in run (line 91)
> evalin('caller', strcat(script, ';'));
>
> Please see attached the code I used, and the associated files of the
> analysis
>
> Thanks in advance for your help!
> Best,
> -Loïc
> PhD candidate
> Vanderbilt University
>
analysis.info
Description: application/info
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