[Eeglablist] Proper Sequence for Manual Rejection, ASR, and ICA in EEG Preprocessing and Related Questions

[Makoto Miyakoshi]

Hi Bong,

> I am concerned about whether ICA can be applied if edges are segmented
due to rejection. Isn't this the reason for performing epoching after ICA?

When ICA starts, it shuffles the time points of the input data. For every
iteration, it shuffles the data differently. So it's not a problem for ICA
that the input data are completely chopped up and even random-ordered in
time (here, you can see the meaning of 'instantaneous independence'; ICA
has no concept of time).

> including EKG might even remove HEP

Why/How does it remove HEP?

Makoto


On Tue, Aug 6, 2024 at 9:09 AM 봉수현 via eeglablist <eeglablist at sccn.ucsd.edu>
wrote:

> I hope this message finds you well. I am currently in the process of
> setting up a preprocessing pipeline for my data and have encountered a few
> questions that I hope you can help me with.
>
> My primary question is regarding the use of Clean_rawdata and where manual
> rejection should be placed in the sequence—should it be performed before or
> after applying Clean_rawdata? Additionally, I am curious whether manual
> rejection should be done before or after ICA.
>
> To provide more context, here is a detailed description of my research
> problem.
> I am attempting to epoch my data based on the latency of the 'R-peak'
> detected in the EKG channel (yes, I am analyzing HEPs). I am considering
> using various algorithms for this purpose, but the Brainbeats package by
> Cannard is currently my top choice due to its remarkable effectiveness in
> my last project.
> However, I sometimes encounter noise in the EKG channel that obscures the
> R-peak, which I plan to reject manually. Since the Brainbeats package
> performs R-peak detection, ICA, and epoching with 'one click,' I am
> considering removing unnecessary segments before this process. This would
> include manually rejecting segments where the R-peak is indistinguishable
> and remove/interpolate frontal lead/leads containing abnormal high
> amplitude noise occationally (I don't know what's problem with these lead).
>
> Given my intention to include such manual rejection, I am unsure about the
> optimal sequence for applying clean_rawdata (ASR), manual rejection, and
> ICA. Specifically, I am concerned about whether ICA can be applied if edges
> are segmented due to rejection. Isn't this the reason for performing
> epoching after ICA?
> Moreover, I would like to know if 'detrending' is necessary for
> experiments similar to mine. FieldTrip tutorials include detrending, but I
> am unsure whether it should be done before or after epoching. 
> Do I need it for my project?
>
> Lastly, regarding the ongoing debate about including EOG and EKG channels
> in ICA: based on my reading, excluding EOG and EKG channels during ICA does
> not significantly impact the results and including EKG might even remove
> HEP (assuming they exist). If there are differing conclusions, I would
> appreciate hearing them.
>
> Thank you for your time and assistance.
> Best regards,
> Bong
>
> Su Hyun Bong, Phd candidate
> KAIST, GSMSE, Korea, Daejeon
> Tel 042-350-4285 Mobile 010-9891-8020 Email 
> npdrbong at kaist.ac.kr mailto:npdrbong at kaist.ac.kr
>
>
> _______________________________________________
> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
> To unsubscribe, send an empty email to
> eeglablist-unsubscribe at sccn.ucsd.edu
> For digest mode, send an email with the subject "set digest mime" to
> eeglablist-request at sccn.ucsd.edu