[FieldTrip] Problems with ft_Channelrepair / interpolation

[Kinkini .]

Hello  Jan,

Thank you so much for your comments.

I am excluding bad channels while applying CAR.
Also, I tried excluding bad channels from ICA and interpolate them later.
But as I had mentioned before, I am facing problems
applying ft_freqstatistics.

Any suggestion on that?

Thanks again,

*Kinkini*


On Sat, May 2, 2020 at 1:51 PM Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Kinkini,
>
> I would recommend not doing a CAR before you have removed bad channels.
> Also, I would recommend not tu ‘repair’ any bad channels prior to running
> ICA.
> Best wishes,
> Jan-Mathijs
>
>
> On 1 May 2020, at 13:33, Kinkini . <bkinkini at gmail.com> wrote:
>
> Dear FieldTripers,
>
> Hope everyone is coping well with the current situation.
>
> I am relatively new in fieldtrip and I have been long stuck with using
> ft_channelrepair for quite sometime now.
>
> Briefly about my analysis pipeline:
> 1- Loading and epoching the data
> 2- ft_preprocessing - filtering, baselining, CAR
> 3- ft_databrowser - marking bad channels
> 4. ft_rejectvisual - rejecting bad channels; keepchannel = 'repair'
> 5. ft_channelrepair
> 6. ICA
> 7. TF Analysis
> 8. TF statististics
>
> I have problems pertaining to step 4 and 5. In step 4 I want to keep the
> bad channels so that I can interpolate them in the next step. When I use
> data browser to look thorough the data, the bad channels look okay. But the
> problem starts when I perform ICA on them. My first observation is that the
> wchange value is very big (looks like this : 257868.69202720), but ICA runs
> completely. However the ICA component topoplots look weird (screenshots
> attached). However, when I look through the icabrowser plots , there are
> peaks at physiological frequencies.
>
> In order to avoid this, I tried getting rid of the bad channels completely
> using ft_rejectvisual, perform ICA and then get back the missing channels
> using neighbourhood average. Doing this, I was able to perform TF analysis,
> but when I wanted to apply statistics on the data, I had errors. Finally, I
> had to avoid the entire step of  interpolation to be able to run everything
> and also perform statistics. But in a long run, I cannot avoid this step.
>
> I am finding no clue as to where is it going wrong.
>
> Hence, any idea, any clue from you all would help me very much. I am happy
> to provide with more details if necessary.
> Thank you so much for your response.
>
> Best regards,
>
> Kinkini Bhadra
> PhD student
> Department of Fundamental Neurosciences
> University of Geneva
>
>
> <Screenshot 2020-05-01 11.57.28.png><Screenshot 2020-05-01 11.57.42.png>
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