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

[Meryem Ayse Yucel]

Hi Jacey,

I'd try lowering STDEVthresh to say 20.

Meryem

> 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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