[FieldTrip] Problems with ft_Channelrepair / interpolation

[Kinkini .]

Hi Jan-Mathijs,

My apologies for providing insufficient information and over generalizing
my question.
But I am happy to let you know that I have just debugged the issue and it
looks like I was having NaN values in some of the trials and
therefore ft_freqstatistics was showing error.

Thanks to you for your previous inputs, it helped me with the problem
related to interpolation and ICA.

Take care,

regards,

*KINKINI BHADRA*


On Sun, May 3, 2020 at 8:46 PM Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Kinkini,
>
> I don’t have any concrete suggestions here. Perhaps you should try and
> first pinpoint the potential cause of the issue yourself. If you dump an
> entire pipeline in an e-mail, it is unclear to us where we should focus on.
> Specifically, it is not clear whether any upstream processing steps are
> relevant at all for the issue you are facing. You wrote: "but when I wanted
> to apply statistics on the data, I had errors”.  This is so ill-conditioned
> that we can just guess as to what is going wrong for you.
> Perhaps consult
> http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community/ to
> phrase your question a bit more to-the-point.
>
> Good luck,
>
> Jan-Mathijs
>
>
> On 2 May 2020, at 22:22, Kinkini . <bkinkini at gmail.com> wrote:
>
> 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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