At 1.19 sec TR, you still only go out to 285 sec, so you will not get condition 8. You should not be playing around with the TR. the TR in the dicom is probably right. Likewise, the paradigm is the paradigm. There's nothing I can really help you with here -- you need to find out for sure what the TR is and what the paradigm is.

On 10/1/2020 2:57 PM, Erica Israel wrote:

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Hi Dr. Greve, 

After looking through my matlab code with the task protocol, I saw that it ended with the rest condition, not the 8th condition. I changed the paradigm file to correct this and changed the TR to 1.19 (which I also double checked). I still got an error with NaN in only the 8th column and row this time but I am searching for anything else I may have missed. If you by chance have any idea what it could be outside of defining the paradigm incorrectly, please let me know, but I am thinking it is something of my own error. Thanks again for all of your time and help. 


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

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Freesurfer@nmr.mgh.harvard.edu
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