Problem with Bandpass_Filter_Auxiliary and Prune Channels

[Verena Schäfer]

Hello Nirs Community,

I am a beginner in the field of data processing with Homer3 and I looked everywhere for exact explanations of the functions but found nothing, so I hope that someone here can answer my questions about it:

I have to use the function Bandpass_Filter_Auxiliary. But I can't find any exlpanation about what this function exactly filters and about the diffrences between Bandpass_Filter_Auxiliary and Bandpass_Filter_OpticalDensity?

Furthermore I want to reject bad channels and I think the best way to do it is with the function Prune Channels. I want to compare frequency in third and bottom quartile of the data and if bottom quartile is less than 10% higher the channel is rejected but I don't understand how I can enter my data at dRange (Preset=dRange(1)=1e+04,dRange(1)=1e+07) ?

many greetings

Verena

[Yucel, Meryem]

Verena,

 

Please check out homer3 github wiki to see function details: https://github.com/BUNPC/Homer3/wiki/Processing-Functions

 

Bandpass_Filter_Auxiliary filters the auxiliary measurements, if any, saved in the snirf file, while bandpass_filter_opticaldensity filters all fNIRS measurements converted into OD.

 

Regarding the enprune function, these numbers are based on the range of raw intensity signal and depend on the system you are using. You may calculate, offline, your threshold from the raw signal depending on your criteria, and use those numbers as your range.

 

Hope this helps.

 

Meryem

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[Verena Schäfer]

thanks for the explanations Meryem! 

  Then I want  to use the bandpassFilter on the OD but my problem is that all my data in the display window disappear even if I set the filter to 0.  As soon as I add this filter in the proc stream, I no longer see any data.  What could that be?

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[Yucel, Meryem]

Could you send a snapshot of your processing stream, and optionally a sample snirf file too?

Thanks,

Meryem

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From: homer...@googlegroups.com <homer...@googlegroups.com> on behalf of Verena Schäfer <theana....@gmail.com>
Sent: Thursday, November 12, 2020 4:39:23 AM
To: homer...@googlegroups.com <homer...@googlegroups.com>
Subject: Re: Problem with Bandpass_Filter_Auxiliary and Prune Channels

 

To view this discussion on the web visit https://groups.google.com/d/msgid/homer-fnirs/CAGJ5yVCdgNx0Y-%2BcMXBoaK%2B5ZAEQpfWtbp9u03rxbucZiRYZBA%40mail.gmail.com.

[Verena Schäfer]

Hello Meryem,

 I am sending the raw file of our measurement, the perception of the file and a screenshot of our processing stream.Thank you in advance, I hope that my problem becomes clear.

many greetings,

Verena

To view this discussion on the web visit https://groups.google.com/d/msgid/homer-fnirs/BLAPR03MB56189EC9D9157893623F8276DDE10%40BLAPR03MB5618.namprd03.prod.outlook.com.

[Yucel, Meryem]

Hi Verena,

 

The bandpass function expects all elements (time points) of the data to be finite. The OD input from your data has some “Inf” elements. That is why you are getting this error. And the Inf elements result from the negative values in raw intensity signal (d). One quick fix would be to add a dc offset to all your raw signal to get rid of any negative values. This should not affect your results as you would be looking at changes. Then the filter should work just fine. You can also check with the nirs company, regarding why the system outputs “negative intensity”.

To view this discussion on the web visit https://groups.google.com/d/msgid/homer-fnirs/CAGJ5yVA20i5Nn8j%3DrrwM5egF5q7nwSdkpLeeWrAqLRr9mbbomA%40mail.gmail.com.