[Homer-users] time scale of HOMER2 Data window

[David Boas]

The problem is quite simple! Homer2 presently assumes that data is 
acquired at a constant rate. Looking at your time vector that you 
provided in the .nirs file, I see that the interval between your data 
samples varies between the two values of 0.094 and 0.109 seconds. Even 
worse, the first interval is 0.061 seconds and many functions in homer2 
use this first interval to set the time base for all intervals. This 
explains why the spike is compressed to an earlier time in your HRF.

The fast solution for you is to interpolate your data on to a constant 
time vector and re-create the .nirs file using this new time vector with 
a stable sample rate.

In the future, when homer2 adopts the SNIRF data format, we will update 
the functions to handle non-constant data sample rates.

Anyone who wants to learn more about the Standard NIR data Format can 
read about it at
https://docs.google.com/document/d/1EKEMrB6CxmEGnzI4zi7MugHq318HRaR3M2i_vzRIPFU/edit?usp=sharing
The standard has been created with input from many different academic 
and commercial interests and will soon be adopted.

Please email this list with any questions or suggestions about SNIRF.

Thanks,
David Boas



On 3/19/13 8:58 AM, Borbala Kollod wrote:
> Hello All!
>
> I have some clarification questions about the the scales of the Data window and the mechanism of HRF block averaging.
> For the scale I guessed  the 'y' axis in concentration view would refer to mikroMols of conc. chaneges. The 'x' axis would refer to time in seconds.
> But then I have this strange result for a channel (attached jpeg) that in one subject's data I averaged 3 trials of the 'blue' condition, and in the HRF I got a huge dip of concentration around 14s after stim onset. Checking the Time course view this huge dip is present after the 3rd trial, but not at 14s after stim onset but later, around 22s. If I exclude the 3rd trial, the dip disappears from the HRF.
> I used the default precessing stream (also attached). Also the datafile is attached, the above mentioned channel is the one between detector3 and sourceB.
>
>
> Can anybody give a cue of that difference in time course view and HRF view?
> Checking the data with another program it seems that the time course view is correct and the tricky part is the HRF view.
>
> Thanks,
> Bori Kollod
>
>
>
>
>
>
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