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HRF Resting state extraction


Monica Crotti
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Hi Meryem,

I was wondering if you could provide me any help regarding the extraction of the HRF from a dataset of a resting state NIRS acquisition.

I tried to add a stimulus at the beginning in order to be able to extract it but this does not work. I am currently stuck and I do not know how to proceed. You can find attached the data from subj 1 of my sample.

Thank you in advance 

Monica

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Meryem Yücel
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Hi Monica,

 

I suspect, since you have a resting data, you want to get the whole concentration time course not an HRF, is that correct?

If so could you try either of these and let me know how it goes?

 

1) Once you run the processing stream, it will create a .mat file with a filename that matches the name of each individual snirf file. If you load this .mat file in matlab, then you will see a variable name "output" in your workspace. This should have the dc time course: output.dc.dataTimeSeries

2) If you run at group level and have the groupResults.mat file, you can follow the steps at the below link to access dc

https://github.com/BUNPC/Homer3/wiki/Output-Files

 

Hope this helps.

 

Meryem

p.s. I did not see any attachment to your post.

 

 

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Monica Crotti
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(@monica-crotti)
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Dear @mayucel,

Thank you very much for your fast reply and I apologize the attachment was not uploaded correctly. I think it is over the maximum size allowed.

I tried to run the prep but I only able to get a Group.results.mat file even if I am not running the group analysis. I am actually working with the version of Homer2. Thus this can also be different and one of the reason I am not able to solve the problem.

 

Thank you again

Best 

Monica

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Oumaïma Benkirane
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Joined: 1 year ago

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Dear @mayucel,

Thanks for the explanations. I am in the exact same situation as @monica-crotti and I managed to have access to the dc time course for each single run. But I don't understand clearly this file. As I have 26 optodes and a file with 78 columns (=26 x3), I guess that every column represents a canal for each of the HbO, HbR and HbT, does this make sense ? If it is the case, as the columns are not labelled (as shown in the joint file), I am not able to know what which column refers to what. 

Thanks in advance,
Oumaïma 

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Meryem Yücel
Posts: 124
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(@mayucel)
Estimable Member
Joined: 2 years ago

Hi Monica,

 

The instructions I gave above were all for Homer3. For your convenience, here are the steps you need to take to extract dc from Homer2 results:

  • You need to load .nirs file in matlab (load filename.nirs -mat)
  • You will see procResult in your work space
  • You can access dc at procResult.dc for that specific run.

(Note that groupResults.mat file has dcAvg for reach run but not dc, hence the above steps.)

Meryem

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