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Hello Freesurfer Experts,
I find a way to do the analysis solving the contrast matrices problem, but I am not sure about this solution, mostly because the results don't look correct to me.
So basically my solution was replicate my 3 runs, and the second time calling it Eccen after the first 3 being polar. This time the contrast matrix was created without any issue and the analyse was done.
So I would like to know if the problem is on my "solution". And if is there any way of doing eccen and polar separately. How should I proceed with this analysis since i use bars that swipe the visual field, from 8 different directions, i think the can be considered as both eccen and polar because I'm covering different angles and different eccentricities.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mesquita, Tiago tiago.mesquita@uni-hamburg.de Sent: 20 April 2024 14:29:19 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Retinotopy error computing contrast matrices
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Hello FreeSurfer Developers,
I am trying to do a retinotopy analysis. My retinotopy has 8 bars, this bars swipe the visual field from the 8 possible directions (all multiple of 45 degrees angle). One complete swipe takes 24 sec. I have 16 different positions per swipe. So I have tried using -retinotopy 24 (period of a complete swipe) or 1.5 (period of each individual bar) in every case i always end up having the same error. For some reason Xcond = NaN (normalized). I tried eccen pos, eccen neg even polar neg and pos in my paradigm files and get always the same result.
Can someone help me? this is what i get:
Creating Design Matrix ... creation time = 0.006 sec DoMCFit = 1 ntptot = 119, nX = 35, DOF = 84 Saving X matrix to ~/Project/Sess02/bold/rtopy.self.lh/pr001/Xtmp.mat XCond = NaN (normalized) Warning: Matrix is singular to working precision.
In fast_selxavg3b (line 403)
Computing contrast matrices Warning: Matrix is singular to working precision.
In fast_selxavg3b (line 441)
Warning: Matrix is singular to working precision.
In fast_selxavg3b (line 441)
OLS Beta Pass run 1 t= 0.0 reading data ... 0.820008 Global Mean 146.10 Global In-Mask Mean = 146.104 (NaN) Rescale Target = 100 RescaleFactor = 0.684444 OLS Residual Pass run 1 t= 0.0 reading data ... 0.776954 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)
Found 7921 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)
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)
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);
If i look into the X.mat m betainc is filled witn NaN.
I have atteched my analysis info and X.mat. Let me know if you need more informations about my analysis.
Best,
Tiago Mesquita