External Email - Use Caution
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., <dgr...@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:
>
> External Email - Use Caution
> 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;
> - the mat file from expanding ring and for rotating wedge (filename:
> expring_SUBJ02_20191122.mat and rotwedge_SUBJ02_20191122.mat).
> <https://drive.google.com/open?id=1vkSRHeTPEn-UE4iighsStYbNkrzn03PG>
> - 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. <
> dgr...@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:
>>
>> External Email - Use Caution
>> 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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>> Freesurfer mailing
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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
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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