<div dir="ltr">Hi Jan-Mathijs,<div><br></div><div>My apologies for providing insufficient information and over generalizing my question. </div><div>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.</div><div><br></div><div>Thanks to you for your previous inputs, it helped me with the problem related to interpolation and ICA.</div><div><br></div><div>Take care,</div><div><br></div><div>regards,</div><div><br></div><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div><b>KINKINI BHADRA</b></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, May 3, 2020 at 8:46 PM Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl">jan.schoffelen@donders.ru.nl</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;">
<font size="4">Hi Kinkini,</font>
<div><font size="4"><br>
</font>
<div><font size="4">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. </font></div>
<div><font size="4">Perhaps consult <a href="http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community/" target="_blank">http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community/</a> to phrase your question
a bit more to-the-point.</font></div>
<div><font size="4"><br>
</font></div>
<div><font size="4">Good luck,</font></div>
<div><font size="4"><br>
</font></div>
<div><font size="4">Jan-Mathijs</font></div>
<div><font size="4"><br>
</font>
<div><br>
<blockquote type="cite">
<div>On 2 May 2020, at 22:22, Kinkini . <<a href="mailto:bkinkini@gmail.com" target="_blank">bkinkini@gmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr">Hello Jan,
<div><br>
</div>
<div>Thank you so much for your comments. </div>
<div><br>
</div>
<div>I am excluding bad channels while applying CAR. </div>
<div>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. </div>
<div><br>
</div>
<div>Any suggestion on that?</div>
<div><br>
</div>
<div>Thanks again, </div>
<div> <br clear="all">
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">
<div><b>Kinkini</b></div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, May 2, 2020 at 1:51 PM Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>Hi Kinkini,
<div><br>
</div>
<div>I would recommend not doing a CAR before you have removed bad channels.</div>
<div>Also, I would recommend not tu ‘repair’ any bad channels prior to running ICA.</div>
<div>Best wishes,</div>
<div>Jan-Mathijs</div>
<div><br>
<div><br>
<blockquote type="cite">
<div>On 1 May 2020, at 13:33, Kinkini . <<a href="mailto:bkinkini@gmail.com" target="_blank">bkinkini@gmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr">Dear FieldTripers,
<div><br>
</div>
<div>Hope everyone is coping well with the current situation.</div>
<div><br>
</div>
<div>I am relatively new in fieldtrip and I have been long stuck with using ft_channelrepair for quite sometime now.</div>
<div><br>
</div>
<div>Briefly about my analysis pipeline:</div>
<div>1- Loading and epoching the data</div>
<div>2- ft_preprocessing - filtering, baselining, CAR</div>
<div>3- ft_databrowser - marking bad channels </div>
<div><font style="background-color:rgb(252,229,205)">4. ft_rejectvisual - rejecting bad channels; keepchannel = 'repair'</font></div>
<div><font style="background-color:rgb(252,229,205)">5. ft_channelrepair</font></div>
<div>6. ICA </div>
<div>7. TF Analysis</div>
<div>8. TF statististics</div>
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>I am finding no clue as to where is it going wrong. </div>
<div><br>
</div>
<div>Hence, any idea, any clue from you all would help me very much. I am happy to provide with more details if necessary.</div>
<div>Thank you so much for your response.</div>
<div><br>
</div>
<div>Best regards,</div>
<div><br>
</div>
<div>
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">Kinkini Bhadra</div>
<div dir="ltr">PhD student</div>
<div>Department of Fundamental Neurosciences</div>
<div dir="ltr">University of Geneva</div>
<div dir="ltr"><br>
<div><b><br>
</b></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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