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Hello, that's a follow up regarding my issue. Do you have any suggestions? Please find enclosed the X.mat file from selxavg3 error (ill conditioned design)

I will test using different parameters. For both expanding ring and rotating wedge 1cycle will last about 50 seconds and each stimulus will have 6 cycles (now I had 1 cycle lasting 200 sec). I guess the error is with timing; I tried to change the duration of 1cycle while doing some test analysis and the commands were performed without errors, so I suppose using the new settings the computation will work.

Thank you for your insight.
Marco

On Tue, 21 Jan 2020 at 16:58, Marco Ninghetto <m.ninghetto@nencki.edu.pl> wrote:
Thank you for your reply. I think I've better explained the situation in a further email, which I paste in here. 

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 it to have 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, 2019
 
To 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 tried to modify, out of curiosity, the duration of 1 cycle lower than 100 seconds in "mkanalysis-sess". It made the job. So I assume that the problem is with that parameter. For further subjects I'll use different timings. But is there still a way to compute calculations on these stimuli?
Moreover, now I acquire only one functional img for each stimulus. Do you recommend me to do more runs? (maybe having only 1 run causes the issue).

Thank you for your help!
Marco





On Tue, 21 Jan 2020, 16:16 Greve, Douglas N.,Ph.D., <DGREVE@mgh.harvard.edu> wrote:
Actually, I was able to get those files from your previous emails

On 1/15/2020 11:24 AM, Marco Ninghetto wrote:

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Sorry for the late reply, the message was non stop bounced.

So, here You will find:
- terminal output for `selxavg3-sess` (filename: terminal_output.txt). I copied only the last part when freesurfer accesses to MATLAB and where the error occurs;
- paradigm files for expanding ring and for rotating wedge

Thank you for your precious help,
Marco

On Fri, 3 Jan 2020 at 17:51, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:
Can you send your paradigm files? Can you also send the terminal output? One more thing, can you send the X.mat file from the output folder?

On 1/2/2020 3:19 AM, Marco Ninghetto wrote:

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Hello experts,
I'm performing retinotopy analysis but when running the command 

    selxavg3-sess

It starts, but after some lines, I get the following error:

    ERROR: design is ill-conditioned

I don't know how to proceed from here to solve the error. 
My retinotopy stimuli make 2 cycles (e.g.: rotating wedge makes 2 full cycles before quit) and each cycle takes 200 seconds to complete. TR is set to 2.5 seconds.

Please, does anyone have any advice?
Thanks in advance,
Marco

--
---------------------------------------------------
Marco Ninghetto, PhD candidate
Laboratory of Neuroplasticity
Nencki Institute of Experimental Biology
Polish Academy of Sciences
3 Pasteur Street, 02-093 Warsaw, Poland

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--
---------------------------------------------------
Marco Ninghetto, PhD candidate
Laboratory of Neuroplasticity
Nencki Institute of Experimental Biology
Polish Academy of Sciences
3 Pasteur Street, 02-093 Warsaw, Poland

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
---------------------------------------------------
Marco Ninghetto, PhD candidate
Laboratory of Neuroplasticity
Nencki Institute of Experimental Biology
Polish Academy of Sciences
3 Pasteur Street, 02-093 Warsaw, Poland