[Mne_analysis] summary performance for ICA

[Denis-Alexander Engemann]

Hi Yu-han,

take a look at this preprocessing script which I wrote to handle ICA for
Neuromag + EEG recordings with maxfilter present.
It's a prototype and might become a function / script at later stages.
Testing + input welcome, I'm trying not to overfilt the recordings from our
lab.

https://gist.github.com/dengemann/da7068af7babdfbf12a2

HTH,
Denis


2014-11-03 21:19 GMT+01:00 Chen, Yu-han <CHENY4 at email.chop.edu>:

>  Hi Dennis,
>
>  Thanks a lot for youre reply. Please see my answers below:
>
>   From: Denis-Alexander Engemann <denis.engemann at gmail.com>
> Date: Monday, November 3, 2014 2:43 PM
> To: The Children's Hospital of Philadelphia The Children's Hospital of
> Philadelphia <cheny4 at email.chop.edu>, "<Mne_analysis at nmr.mgh.harvard.edu>"
> <Mne_analysis at nmr.mgh.harvard.edu>
> Subject: Re: [Mne_analysis] summary performance for ICA
>
>   Hi Yuhan,
>
> I include the mailing list in this part of our conversation because this
> might be interesting for other people as well.
>
>
> 2014-11-03 20:30 GMT+01:00 Chen, Yu-han <CHENY4 at email.chop.edu>:
> >
> > Hi Dennis,
> >
> > I (...) figured out that the SSP was turned on during epoching. Our
> original problem is that when we tried to epoch raw data, ICA cleaned data,
> ECG signal, the averaged ECG epoch is flat (zeros across the entire epoch).
> When we set proj = False for mne.Epoch, the problem is resolved. Is it true
> that by default, Epoch.py will set the SSP on?
> >
>
> Yes, you need to take care of this. Anyways I'm surprised you're getting
> flat signals. What kind of SSPs did you include?
>
>  *** I didn't intentionally include any SSPs when I read in the data so I
> don't know what type of SSP was included.
>
>
> >
> > The data I feed in is the Elekta data with maxfiltered tsss and movement
> correction applied.
> >
>
> Normally you have SSPS included in the raws if you don't use maxfilter.
> But think there's no point in using those if you have maxfiltered your data.
> If you aim to identify biological artifacts using ICA there is no point in
> having ECG/EOG projections.
> When using maxfilter and ICA, you should not necessarily use SSP in
> addition.
> FYI I'd recommend to look up the number of dimensions estimated by
> maxfilter from the log or recover it by estimating the rank of the data and
> using this as input to ICA(n_components).
>
>  *** I wasn't planning to use SSP. In my case the SSPS was off when I
> read in maxfiltered raw data. For some reason when I epoch the raw data, by
> default the SSP was set on. So I think the Epoch.py function just set SSP
> on. Should I always assume the SSP is on when I epoch any type of raw
> Elekta data no matter the maxfilter was applied or not?
>
> *** the n_components I used for ICA is 95% assuming 5% of our data is
> noise. I realized I don't have the number of dimensions extimated from the
> maxfilter log. Is this something I should specifically set when I run
> maxfilter? Also could you please tell e how to get the estimated ran of the
> data?
>
>
>
>
> HTH,
> Denis
>
> PS: what about the performance metric, still interested in contributing
> it? ;-)
>
>  *** I'm still using the exact same code from Juergen and I thought that
> was already shared and uploaded to gitHub?
>
>
> > Thanks!
> > Yuhan
>
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