[Eeglablist] Fwd: ICA weights not "saved"?

[Andrew Hill]

I've not totally figured this out either - when running ICA against a  
Study, i don't seem to be able to save the ICA weights.   If I edit  
the Study and check resave datasets.. the message says they haven't  
changed, don't need to be resaved.. and saving the Study itself  
explicitly doesn't seem to save ICA weights either...

What am I doing wrong?  :)

thanks,
andrew

On Aug 19, 2009, at 9:22 AM, Keith Yoder wrote:

> Since two of us have encountered this issue before, it's probably  
> worth posting this to list.
>
> ---------- Forwarded message ----------
> From: Keith Yoder <kjyoder at gmail.com>
> Date: Thu, Aug 13, 2009 at 5:21 PM
> Subject: Re: [Eeglablist] ICA weights not "saved"?
> To: Andrew Hill <andrewhill at ucla.edu>
>
>
> In our case, we have to restrict the amount of data that ICA is  
> working with to produce sensible components, but this is certainly  
> driven in large-part by our paradigm.  We are having subjects play a  
> video game that consists of four distinct minigames, each of which  
> has one or more cognitive tasks built into it (for more information  
> see http://autismcollaborative.org).
> This has given us very large datasets (128 channels recording for an  
> hour).  I thought this would be great - ICA would have a *lot* of  
> data to work with.  However, this means that the specfic events we  
> are interested in comprise a very small proportion of the EEG data  
> individually.  For instance, a go-no-go task in one of the minigames  
> occurs less than 60 times per game.  If I'm assuming that the  
> salient effects in the EEG occur within a three second window at  
> each event, then I'm expecting ICA to pick out components that may  
> only be active for for a total of 3 minutes out of the hour.
> -Keith
>
> On Thu, Aug 13, 2009 at 4:40 PM, Andrew Hill <andrewhill at ucla.edu>  
> wrote:
> hi Keith,
>
> thanks for the reply - explicitly saving after ICA weights are  
> calculated is what i was missing.
>
> on running the ICA on epochs versus continuous recordings.. I was  
> under the impression that Arno and Scott encouraged running ICA on  
> the "longest" data chunks possible, and that running them on epochs  
> would actually produce artifacts at the edges of the epoch.. are you  
> not finding this?
>
> best,
> andrew
>
> On Aug 11, 2009, at 5:41 AM, Keith Yoder wrote:
>
>> I had a similar experience at first.  Here's my resolution:
>> Once Run ICA is finished, manually save the component-weighted  
>> datset.  This can be done by either 'File -> save current  
>> dataset(s) as' or, if you are using a script, the pop_saveset(EEG)  
>> command.
>> A rough outline of our process:
>> Import the dataset
>> Highpass filter the dataset
>> Save that filtered dataset
>> Extract epochs
>> Save the epoched datasets
>> Run ICA
>> Save the component-weighted epoched datasets
>> We've found that running ICA before epoching the datasets yields  
>> nonsensical results.  Additionally, if you epoch the data first,  
>> then the ICA algorithm will only have to work on the data  
>> surrounding your event of interest.  This will can greatly reduce  
>> the amount of time required for the algorithm to identify  
>> components.  If your events are widely spaced throughout the  
>> dataset, you may even be able to include all of your channels at  
>> once.
>> Hope this helps!  If you have any questions, feel free to let me  
>> know.
>> -Keith
>> Research Aide
>> Belmonte Autism Lab
>> Cornell University
>>
>> On Mon, Aug 10, 2009 at 3:49 PM, Andrew Hill <andrewhill at ucla.edu>  
>> wrote:
>> hi folks,
>>
>> i might be misunderstanding something about how the "Run ICA" works.
>> i've been running ICA against .set files, half of the channels at a
>> time to avoid out of memory errors... i got through all my .sets, and
>> then extracted epochs from all the .set files, assuming the ICA
>> weights would be inherited by the epochs.
>>
>> the problem is, when i open one of these .set files, it appears that
>> the data file doesn't actually have ICA weights saved into it. am i
>> doing something wrong??  is there some step to explicitly save the
>> weights with the .set file that i need to do?
>>
>> these weights don't appear to be saved even with the "write ICA
>> activations to disk" option checked...
>>
>> i cannot load more than one .set into memory at a time... and i  
>> cannot
>> process more than half the channels in one Run ICA go.. so what am i
>> missing?  why are these not saved to the .set?
>>
>> thanks,
>> andrew
>>
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>
>
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