External Email - Use Caution
Hello, I'm analyzing retinotopy data. I used expanding ring and rotating wedge. For my pilot, unfortunately, we used only 2 cycles for each stimulus and 1 cycle lasted 200 seconds (for sure I will change to more cycles lasting less). TR = 2.5.
Retinotopy paradigm files are as follow: -for expanding ring (pos direction since it expands): stimtype eccen direction pos -for rotating wedge (neg direction since is counter-clockwise): stimtype polar direction neg
To compute analyses, I ran the following pipeline: 1) recon-all 2) preproc-sess 3) mkanalysis-sess 4) selxavg3-sess Having only two cycles for each stimulus, in mkanalysis-sess, I used the option -hpf and lowered the filter to 0.5.
In the last level (selxavg3-sess), I get the error. Basically this step runs up to when MATLAB starts to calculate. Here I get the following error:
MATLAB is selecting SOFTWARE OPENGL rendering.
< M A T L A B (R) > Copyright 1984-2019 The MathWorks, Inc. R2019b Update 3 (9.7.0.1261785) 64-bit (glnxa64) November 27, 2019To get started, type doc. For product information, visit www.mathworks.com.
> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
/usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m
> starting fast_selxavg3b
#@# SUBJ02 ############################### /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
outtop = /media/sf_w_Desktop/w_pRF/retinotopy Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 11, skipping nruns = 2 autostimdur =
outanadir = /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02/bold/retinotopy.lh Found 118266/125623 (94.1) voxels in mask 1 Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 260, nX = 158, DOF = 102 Saving X matrix to /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02/bold/retinotopy.lh/Xtmp.mat XCond = 6.85663e+16 (normalized) ERROR: design is ill-conditioned ans = 1
ERROR: fast_selxavg3() failed\n
I'm stuck with analyses and I cannot proceed further. Could you provide some insight on what to do? Having only two long lasting cycles, do I have to use further optional flags in my commands? Thank you for your time, Marco
External Email - Use Caution
Sorry for the further message. I checked the x.mat file and it seemed that the command only read one rtopy.par file. So now I modified the parameter file from this:
*stimtype eccen*
*direction pos*
to this:
*stimtype eccen* *direction pos *
I modified the parameter file for polar, too. Now, checking the X.mat file I have both of the stimuli taken into account. But I came up with a new error, which I post below.
MATLAB is selecting SOFTWARE OPENGL rendering.
< M A T L A B (R) > Copyright 1984-2019 The MathWorks, Inc. R2019b Update 3 (9.7.0.1261785) 64-bit (glnxa64) November 27, 2019To get started, type doc. For product information, visit www.mathworks.com.
> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
/usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m
> starting fast_selxavg3b
#@# SUBJ02 ############################### /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
outtop = /media/sf_w_Desktop/w_pRF/retinotopy Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 11, skipping nruns = 2 autostimdur =
outanadir = /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02/bold/retinotopy.lh/pr001 Found 118266/125623 (94.1) voxels in mask 1 Creating Design Matrix ... creation time = 0.005 sec DoMCFit = 1 ntptot = 130, nX = 91, DOF = 39 Saving X matrix to /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02/bold/retinotopy.lh/pr001/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);
In addition to the X.mat file, I attached my actual rtopy.par files for eccentricity and for polar. What's wrong now? Sorry for the confusion. I really appreciate your help in this matter, Marco
On Fri, 17 Jan 2020 at 13:35, Marco Ninghetto m.ninghetto@nencki.edu.pl wrote:
Hello, I'm analyzing retinotopy data. I used expanding ring and rotating wedge. For my pilot, unfortunately, we used only 2 cycles for each stimulus and 1 cycle lasted 200 seconds (for sure I will change to more cycles lasting less). TR = 2.5.
Retinotopy paradigm files are as follow: -for expanding ring (pos direction since it expands): stimtype eccen direction pos -for rotating wedge (neg direction since is counter-clockwise): stimtype polar direction neg
To compute analyses, I ran the following pipeline:
- recon-all
- preproc-sess
- mkanalysis-sess
- selxavg3-sess
Having only two cycles for each stimulus, in mkanalysis-sess, I used the option -hpf and lowered the filter to 0.5.
In the last level (selxavg3-sess), I get the error. Basically this step runs up to when MATLAB starts to calculate. Here I get the following error:
MATLAB is selecting SOFTWARE OPENGL rendering.
< M A T L A B (R) > Copyright 1984-2019 The MathWorks, Inc. R2019b Update 3 (9.7.0.1261785) 64-bit (glnxa64) November 27, 2019To get started, type doc. For product information, visit www.mathworks.com.
>> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
/usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m
>> starting fast_selxavg3b
#@# SUBJ02 ############################### /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
outtop = /media/sf_w_Desktop/w_pRF/retinotopy Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 11, skipping nruns = 2 autostimdur =
outanadir = /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02/bold/retinotopy.lh Found 118266/125623 (94.1) voxels in mask 1 Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 260, nX = 158, DOF = 102 Saving X matrix to /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02/bold/retinotopy.lh/Xtmp.mat XCond = 6.85663e+16 (normalized) ERROR: design is ill-conditioned ans = 1
ERROR: fast_selxavg3() failed\n
I'm stuck with analyses and I cannot proceed further. Could you provide some insight on what to do? Having only two long lasting cycles, do I have to use further optional flags in my commands? Thank you for your time, Marco
--
Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland
freesurfer@nmr.mgh.harvard.edu
-
Marco Ninghetto