[Homer-users] parameters for identifying motion artifact and the influences of bad channels

[Jacey Chen]

Hi Sabrina
thank you very much for your email. Following your suggestion, I removed
other functions and tried the results, but kept getting the same results
until I removed the stim_exclude function. After that, I used the
processing stream with all the other functions included but removing the
stim_exclude function on another subject. The stim marks turned to be solid
line (it should be, because the stim_exclude function has been removed),
but I still feel the the motion artifacts were marked wrong. I am attaching
another screen shot, and you can see that some motion artifact were so
obvious, but they have not been marked. Is there any other parameter wrong?


On Thu, Jul 11, 2013 at 4:36 AM, Sabrina Brigadoi <
sabrina.brigadoi at gmail.com> wrote:

> I Jacey,
>
> hmrMotionArtifactByChannels acts only on the active channels and does not
> take into account the pruned ones.
>
> To try to isolate your problem, have you tried to perform the processing
> stream with only the prune channels and the motion artifacts by channels
> functions removing all other functions you are using? What do you get? The
> same results?
>
> Sabrina
>
>
> 2013/7/10 Jacey Chen <jiech at umich.edu>
>
>> Dear Hommer-users
>> I have a question regarding the amp thresh on the motion artifact
>> detection.
>> As I remembered from the Homer training and some other articles, it was
>> usually set as 0.4 or 0.5. However, in our data, I tried different numbers
>> from 0.5 to 3 in the ampthresh and the motion artifact detection always
>> marked the whole data set as a motion artifact and excluded all of the stim
>> marks. (Although when I changed the ampthresh number to 5 and the marks
>> were gone, I don't know how to justify the parameter we set).
>>
>> When I took at the individual channel separately, I saw the motion
>> artifact marks only appeared in the bad channels which we have already
>> excluded. I do not understand why the excluded channels still influence the
>> stim mark rejection, and would like to see if anyone got the similar
>> problem and how to solve that.
>>
>> I am attaching the screen shot here: Capture1.png shows that all the stim
>> marks were excluded after processing motion_artifacts_by_Chanel (dashed dot
>> for the stim mark). The second graph (motion by channel good channel) shows
>> when the "motion by channel" option was checked, no motion artifact was
>> marked in these good channels (but the stim mark was still in dashed dot).
>> The third graph (motion by channel bad channel) further revealed that the
>> motion artifacts only happened in this bad channel which may result in
>> excluding all the stim marks.
>>
>> To sum up, although the bad channels have been excluded, the motion
>> artifact and stim mark rejection seems to still depend on all the channels
>> even though we chose "motion_artifacts_by Chanel" for the motion artifact
>> detection. Is there anyway to have the bad channel out of all the analyses
>> even for the motion artifact detection? Or is there anything I did wrong?
>>
>> Thank you!!
>>
>> --
>> Postdoctoral Research Fellow
>> Center for Human Growth and Development
>> Department of Psychology
>> University of Michigan
>>
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>
>
> --
> Sabrina Brigadoi
> sabrina.brigadoi at gmail.com
>
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-- 
Postdoctoral Research Fellow
Center for Human Growth and Development
Department of Psychology
University of Michigan
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