[FieldTrip] Independent component analysis (ICA) to remove EOG artifacts

[Elif Tülay]

Hi Erfan,

Actually, I could not guess the reason for the error right now, It could be
because of your data format, because of the FieldTrip version, or a
completely different reason :) I can only suggest trying to define
cfg.colormap manually if you haven't done it yet. You can assign a string
for colormap. If I am not wrong, the recommended colormaps include
'parula', 'cividis', 'balance',and '*RdBu'. However, you can find more from
the link below.

https://urldefense.com/v3/__https://github.com/fieldtrip/fieldtrip/blob/master/plotting/ft_colormap.m__;!!HJOPV4FYYWzcc1jazlU!7_vQHuRJZ7C2_jEZ-7PdDNKGgdpAwN3zAS8rdYwAGytoJXLC_2TXcxM-7bN5pa86SUEIc9hPnIhO-pXCls4GlpCFBg$ 

I hope it works.



On Tue, May 9, 2023 at 10:13 PM Erfan Vi via fieldtrip <
fieldtrip at science.ru.nl> wrote:

> Hi Elif,
>
> I get the following error while using the ft_databrowse function:
>
> Undefined function 'ft_colormap' for input arguments of type 'char'.
>
> Error in ft_databrowser (line 686)
>     cfg.colormap = ft_colormap(cfg.colormap);
>
> Do you know how to fix it?
>
> Thank you for your attention to my problem.
>
> On Sun, May 7, 2023 at 1:48 PM Elif Tülay via fieldtrip <
> fieldtrip at science.ru.nl> wrote:
>
>> Hi Erfan,
>>
>> Maybe I can suggest a way to try until a technical answer comes from Jan.
>> If you are familiar with your data, you can detect the bad channel by
>> visual inspection using ft_databrowse. After that, while you are running
>> ICA, you can exclude the bad channel with the following format (you can
>> modify it according to your data)
>>
>>
>>
>> *     cfg.channel = {'all','-Cz'} %just an example for excluding Cz from all channels*
>>
>> I hope it works for you
>>
>> Best
>>
>>
>> On Sun, May 7, 2023 at 12:41 PM Erfan Vi via fieldtrip <
>> fieldtrip at science.ru.nl> wrote:
>>
>>> Hi Jan,
>>>
>>> Thank you for your clear response. How can I determine the name of this
>>> bad channel which is recognizable in the forwarded image? I am new to
>>> FildTrip sorry for the basic questions.
>>>
>>> Erfan-Vajdi
>>>
>>> On Thu, May 4, 2023 at 11:01 AM Schoffelen, J.M. (Jan Mathijs) via
>>> fieldtrip <fieldtrip at science.ru.nl> wrote:
>>>
>>>> Hi Erfan,
>>>>
>>>> These results look like a classical example of a bad channel. If you
>>>> remove this channel from the data prior to running the IC decomposition,
>>>> results should look more sensible.
>>>>
>>>> Good luck,
>>>> Jan-Mathijs
>>>>
>>>>
>>>> On 29 Apr 2023, at 11:04, Erfan Vi via fieldtrip <
>>>> fieldtrip at science.ru.nl> wrote:
>>>>
>>>> Dear FieldTrip users,
>>>> I have used an example script in the
>>>> FieldTrip site to remove EOG artifacts for MEG data example located at
>>>> https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/example/ica_eog/__;!!HJOPV4FYYWzcc1jazlU!7_vQHuRJZ7C2_jEZ-7PdDNKGgdpAwN3zAS8rdYwAGytoJXLC_2TXcxM-7bN5pa86SUEIc9hPnIhO-pXCls4BDwDb8w$ 
>>>> <https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/example/ica_eog/__;!!HJOPV4FYYWzcc1jazlU!8RVcT7vt9rwPHgbzvPH5IFv1KhvliFf9uclvd7fGeD9y3jTEiNhEtGq3rVOa03BcW9lZ3qoBc324h57I8PtCyKZbyA$>
>>>> using ICA. But I got poor results as below image. Any one can help me?
>>>> Thank you,
>>>>
>>>> <ICA.jpg>
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