Re: [Freesurfer] selxavg3-sess failed

[Greve, Douglas N.,Ph.D.]

It does not look like the error was captured in the log file. Can you send the 
full terminal output?
On 6/2/2019 5:02 AM, starxifd wrote:

External Email - Use CautionIt

Hi, FS experts
I got into trouble when running  ’selxavg3-sess’ with a session id file. All 
sessions specified in sessid file. To do 1st-level GLM analysis, I used the 
following command:
Selxavg-sess -sf sessid -analysis stereo.sm5.lh
Then I was told “Matlab is exiting because of fatal error …… 
ERROR:fast_selxavg3() failed\n”  The log is attached in the mail.
However, I run selxavg3-sess with only one session successfully. (Command: 
Selxavg3-sess -s HC025 -analysis stereo.sm5.lh)
I wonder if there was something wrong with my Matlab (version R2014b) or other 
procedures?
Any advice will be appreciated! Thx!

The whole procedure I did:
preproc-sess -sf sessid -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 
5 -per-run
mkanalysis-sess -fsd bold -analysis stereo.sm5.lh -surface fsaverage lh -fwhm 5 
-paradigm stereo.par -event-related -spmhrf 0 -refeventdur 16 -polyfit 2 
-mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run
mkcontrast-sess -analysis stereo.sm5.lh -contrast 3d-v-non3d -a 1 -c 2
Selxavg-sess -sf sessid -analysis stereo.sm5.lh
Star



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Re: [Freesurfer] selxavg3-sess failed

[Douglas N Greve]

These are often very hard problems to track down so please send a full 
bug report

surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

doug


mi...@nmr.mgh.harvard.edu wrote:
> Hello All,
>
> I'm getting an error similar to another some months back.
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09729.html
>
> The command is failing on 2 of our subjects, but running properly for
> others. For the 2 failed sessions, it's creating only the dof and Xtmp.mat
> files in the analysis directory. I have pasted the ending output below.
> Any input on how to resolve this is appreciated. Thanks!
>
> Marlisa Isom
> Research Assistant
> Manoach Lab
> (617) 726-1908
>
> Warning: Matrix is singular to working precision.
>   
>> In fast_selxavg3 at 212
>> 
> Warning: Matrix is singular to working precision.
>   
>> In fast_selxavg3 at 212
>> 
> Warning: Matrix is singular to working precision.
>   
>> In fast_selxavg3 at 212
>> 
> ntptot = 948, nX = 132, DOF = 816
> Saving X matrix to
> /autofs/space/ventzl_036/users/RespMon12C/subjects/RMCON011/bold/RM_prep/Xtmp.mat
> ??? Error using ==> svd
> Input to SVD must not contain NaN or Inf.
>
> Error in ==> cond at 40
>s = svd(A);
>
> Error in ==> fast_selxavg3 at 248
>   XCond = cond(XtX);
>
>   
>>> --
>>>   
> ERROR: fast_selxavg3() failed\n
>
>
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>
>
>   

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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[Freesurfer] selxavg3-sess failed

[misom]

Hello All,

I'm getting an error similar to another some months back.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09729.html

The command is failing on 2 of our subjects, but running properly for
others. For the 2 failed sessions, it's creating only the dof and Xtmp.mat
files in the analysis directory. I have pasted the ending output below.
Any input on how to resolve this is appreciated. Thanks!

Marlisa Isom
Research Assistant
Manoach Lab
(617) 726-1908

Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 212
Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 212
Warning: Matrix is singular to working precision.
> In fast_selxavg3 at 212
ntptot = 948, nX = 132, DOF = 816
Saving X matrix to
/autofs/space/ventzl_036/users/RespMon12C/subjects/RMCON011/bold/RM_prep/Xtmp.mat
??? Error using ==> svd
Input to SVD must not contain NaN or Inf.

Error in ==> cond at 40
   s = svd(A);

Error in ==> fast_selxavg3 at 248
  XCond = cond(XtX);

>> --
ERROR: fast_selxavg3() failed\n


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