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

[Jacey Chen]

If hmrMotionArtifactByChannels acts only on the active channels, I should
see the differences when I manually exclude some channels, right? But it is
not the case. I excluded all the other channels and only kept one channel
active, but the stim marks were still dashed even though no motion artifact
was marked under this channel. I don't understand why it happened. Does
anyone have the answer?
Thank you!!


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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