[FieldTrip] Problems with ft_Channelrepair / interpolation

[Schoffelen, J.M. (Jan Mathijs)]

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<mailto: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


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