[FieldTrip] Fwd: Problem with ICA using data exported via Brainvision analyser

[Max Cantor]

I just realized I accidentally forgot to do reply all and the subsequent
responses weren't posted on the mailing list, so I'm forwarding it back on
for anyone else who was following. Sorry!

---------- Forwarded message ----------
From: Max Cantor <mcantor at umich.edu>
Date: Thu, Jan 30, 2014 at 9:24 AM
Subject: Re: [FieldTrip] Problem with ICA using data exported via
Brainvision analyser
To: Hwee Ling Lee <hweeling.lee at gmail.com>


I'm not sure I understand what you mean by not being able to find the data
that corresponds to the reference channel. For your call to
ft_componentanalysis, for cfg.channel, if you set it to {'all',
'-refchan'}, where refchan stands for whatever your reference channel is
called, that should remove the reference channel from ICA. If you're issue
is what I think it is, this tutorial should reiterate what I'm talking
about:

http://fieldtrip.fcdonders.nl/faq/why_does_my_ica_output_contain_complex_numbers

Sorry if I'm misunderstanding the problem you're having, but hopefully this
clarifies things.


On Thu, Jan 30, 2014 at 8:35 AM, Hwee Ling Lee <hweeling.lee at gmail.com>wrote:

> Dear Max,
> Thanks for taking your time to explain this. I would like to try your
> suggestion, but the problem is that i don't know which channel i should
> remove from my data since i can't find the data that corresponds to the
> reference channel.
> The funny thing for me at least is that this problem does not occur when i
> use the raw data that has not been exported by brainvision analyser. I'll
> try to look at the archives regarding this.
> Thanks again.
> Cheers,
> Hweeling
>  On 30 Jan 2014 13:54, "Max Cantor" <mcantor at umich.edu> wrote:
>
>> Hm, did you try it? I had a similar issue awhile back and that solved it
>> for me. Let me see if I can explain this correctly: I think the fact that
>> there is no data from the reference channel is exactly the problem. ICA is
>> performing a transform on the data, 'rotating' the data from channel space
>> to component space, based on rank. If there is no data in any of the
>> channels, you're asking ICA to transform the data into more components than
>> effectively there are channels; in other words the dimensions in the
>> 'rotation' of the data (if you think of the transform like a geometric
>> rotation) are off. Hopefully that explanation makes sense, or somebody else
>> can explain it more adequately. I think somewhere in the archives there was
>> a long thread about ICA where I and a few other people ask about this
>> issue, so that may help as well.
>>
>>
>> On Thu, Jan 30, 2014 at 5:58 AM, Hwee Ling Lee <hweeling.lee at gmail.com>wrote:
>>
>>> Hi Max,
>>>
>>> Thanks for your suggestion. However, I checked the data, there was no
>>> data from the reference channel, so I doubt this is the problem for the
>>> rank issue.
>>>
>>> Cheers,
>>> Hweeling
>>>
>>>
>>>
>>> On 29 January 2014 15:31, Max Cantor <mcantor at umich.edu> wrote:
>>>
>>>> Hi Hwee,
>>>>
>>>> It may be your reference channel. Try removing your reference channel
>>>> from ICA and it should resolve the rank issue.
>>>>
>>>> Max Cantor
>>>> Research Assistant
>>>> Computational Neurolinguistics Lab
>>>> University of Michigan
>>>>
>>>>
>>>> On Wed, Jan 29, 2014 at 8:57 AM, Hwee Ling Lee <hweeling.lee at gmail.com>wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> Whenever I export my EEG data using Brainvision analyser, I get
>>>>> problems with running ICA on Fieldtrip. The data has a different rank,
>>>>> although I specify to compute ICA using all channels.
>>>>>
>>>>> However, when I use the raw EEG data collected from Brainvision
>>>>> recorder, I do not get this problem.
>>>>>
>>>>> Does anyone know why and how to resolve this issue?
>>>>>
>>>>> My purpose of using Brainvision analyser is to downsample the EEG raw
>>>>> data before further analyses.
>>>>>
>>>>> Thanks.
>>>>>
>>>>> Best regards,
>>>>> Hweeling
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> fieldtrip mailing list
>>>>> fieldtrip at donders.ru.nl
>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> =================================================
>>> Dr. rer. nat. Lee, Hwee Ling
>>> Postdoc
>>> German Center for Neurodegenerative Diseases (DZNE) Bonn
>>>
>>> Email 1: hwee-ling.lee<at>dzne.de
>>> Email 2: hweeling.lee<at>gmail.com
>>>
>>> https://sites.google.com/site/hweelinglee/home
>>>
>>> Correspondence Address:
>>> Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
>>> =================================================
>>>
>>
>>
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