External Email - Use Caution
Hi Loïc,
Uncertain if this will address the error you are receiving, but after looking
over your analysis.info files and the analysis script, it looks like you are
trying to analyze each individual retinotopy run (polar or eccen) separately?
If that is your intention, then you should include a runlist flag with your
mkanalysis-sess command. With no runlist pointing the analysis to a single run
to analyze the selxavg3-sess includes all the runs it finds within the fsd
(bold subdir), and it looks for the run name specific paradigm file in each run
folder which probably doesn’t exist in each run subdir.
Typically one includes all the retinotopy runs of a specific type when looking
to get eccen or polar maps. In that case you would just need paradigm files
present in each run folder which all have the same name and a run list
identifying all the eccen or polar runs. If you still encounter errors, it
might be helpful to see what information is contained in the paradigm files you
are using.
Lastly, I noticed that the retinotopy period differs across the two
analysis.info files you had sent out (30 vs. 32), just FYI.
-Louis
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Loïc Daumail
<loic.daum...@gmail.com>
Date: Monday, June 5, 2023 at 5:35 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Error with running retinotopy glm
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<mailto: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
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