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I changed TR to 1.25 since the full run is 300 seconds, but then only the 8th condition was not being presented it seemed. So I tried 1.33 if the issue was that the paradigm does not end with the null condition, so it could be looking for 8conditions*20seconds each*2? The output to that was: ERROR: TR mismatch between analysis and data

analysis TR = 1.33, data TR = 1.19


ans =


     1
I tried 1.19 as well, and had the same error as the original. Am I most likely missing accurate paradigm information?
I've attached the xtmp.mat file again.

Thank you.

On Wed, Sep 30, 2020 at 1:59 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
It looks like the problem is that condition 8 is never presented. There are 240 time points in the run. At a TR of 1.08, the run ends at 259.2 seconds, so neither condition 7 nor 8 are actually presented.

On 9/28/2020 3:12 PM, Erica Israel wrote:

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Hi there,

I am having trouble running the selxavg3-sess command, in which I am receiving the error:

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);


I assume it has something to do with my paradigm file, but was not able to figure out the main issue as I keep getting the same error after changing possible problems in the file (extra characters, changing to plain txt etc.)


Looking into the Xtmp.mat file, I saw that only the 7th and 8th rows and columns consisted of NaN but am not sure how to interpret this. Below is what my paradigm file looks like and my Xtmp file is attached. 


  0.0000    0    20.00   1.0 rest

  20.000    1    20.00   1.0 thumbab

  40.000    0    20.00   1.0 rest

  60.000    2    20.00   1.0 thumbflex

 80.0000    0    20.00   1.0 rest

 100.000    3    20.00   1.0 thumbrot

 120.000    0    20.00   1.0 rest

 140.000    4    20.00   1.0 index

 160.000    0    20.00   1.0 rest

 180.000    5    20.00   1.0 digits

 200.000    0    20.00   1.0 rest

 220.000    6    20.00   1.0 wristProSup

 240.000    0    20.00   1.0 rest

 260.000    7    20.00   1.0 elbowFlex

 280.000    0    20.00   1.0 rest

 300.000    8    20.00   1.0 wristFlex


Additionally, here is an example of what I ran to make one of the analysis sessions: 

mkanalysis-sess -fsd left -stc up  -surface self lh -fwhm 5 -event-related -paradigm ParadigmFile -nconditions 8 -spmhrf 0 -TR 1.08 -refeventdur 20 -nskip 4 -polyfit 2 -analysis left_arm.lh -per-session -force


Thank you for the help!


--
Erica Israel
Senior Research Support Associate 
MIT Media Lab - Biomechatronics Group 

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Freesurfer mailing list
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--
Erica Israel
Senior Research Support Associate 
MIT Media Lab - Biomechatronics Group