[Homer-users] HRF Plot

[David Boas]

Another thing to check for is whether any stim trials were included. You 
will get a blank HRF if there are no stim marks indicating the onset of 
a stimulus.

When I look at your data, in fact the motion artifact detection function 
has marked the whole data set as a motion artifact and as a result has 
excluded all of your stim marks. The data looks very noisy, but perhaps 
that is deceiving because it seems you put OD into the d matrix in the 
.nirs file rather than intensity. Your raw data has negative values. 
Since it is not possible to have a negative intensity of light, Homer2 
will misbehave when trying to convert negative intensities of light to a 
change in OD.

Steps to try:
1) put intensity into the d matrix in the nirs file, not OD.
2) change the amp thresh on the motion artifact detection function.
3) set a low pass filter to 0.5 Hz for smooth out the noise more.



On 3/22/13 10:09 AM, Meryem Ayse Yucel wrote:
> Have you clicked on one of the channels on the top right corner of
> EasyNIRS gui? Otherwise it will show nothing. (In the image you sent, it
> does not seem to be so).
>
> Meryem
>
>
>
>> Hi all,
>>
>> I have a question about plotting an hemodynamic response function.
>>
>> NIRS data has been recorded with an ISS Imagant (srate=19.5312Hz) and
>> then, converted to the nirs-format (according to the manual). I used
>> Homer2 (v1.5) and loaded the standard config file. Then, I processed the
>> data based on the standard options (see attached file: options.png).
>> After processing all 30 datasets, I'd like to view the HRF. So, I select
>> "show Run HRF" on Conc-data. Unfortunately, the plot window remains
>> empty. Homer2 doesn't show any error messages.
>>
>> I uploaded an example dataset, which contains data of one out of three
>> probes (all thee probes would take too much space...). It can be
>> downloaded from (39.3MB):
>> http://www.stud.uni-karlsruhe.de/~uubuq/subj06_run02.nirs
>>
>> This dataset only contains 3 out of 5 different conditions (i.e.
>> condition 1, 2 and 3. Conditions 4 and 5 are in other datasets). When
>> plotting the HRF, I am expecting an increase only in condition 1.
>>
>> I would really appreciate if anyone could have a look at it.
>>
>> Thank you in advance!
>>
>> Best Regards,
>> Sebastian Hesslinger
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