<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Thanks Stephen and Jan-Mathijs,<div class=""><br class=""></div><div class="">You’re both right. I don’t think ft_channelrepair is the right way to restore a missing channel for MEG data. The situation was that a dataset was recorded with a few malfunctioning channels, which were turned off since their bad signal seemed to be invading other channels. This was for a subset of subjects. We didn’t want to lose the data, so ft_channelrepair was attempted, which revealed the odd functionality. In the end, I agree with Stephen that Maxfilter is the way to go. I found this, which is helpful for understanding how to do this:</div><div class=""><br class=""></div><div class=""><a href="http://imaging.mrc-cbu.cam.ac.uk/meg/InterpolateData" class="">http://imaging.mrc-cbu.cam.ac.uk/meg/InterpolateData</a></div><div class=""><br class=""></div><div class="">My ESI address it still working. I got the bug CC.</div><div class=""><br class=""></div><div class="">Best,</div><div class=""><br class=""></div><div class="">C.<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 7. Apr 2019, at 12:00, <a href="mailto:fieldtrip-request@science.ru.nl" class="">fieldtrip-request@science.ru.nl</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Send fieldtrip mailing list submissions to<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a><br class=""><br class="">To subscribe or unsubscribe via the World Wide Web, visit<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">or, via email, send a message with subject or body 'help' to<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>fieldtrip-request@science.ru.nl<br class=""><br class="">You can reach the person managing the list at<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>fieldtrip-owner@science.ru.nl<br class=""><br class="">When replying, please edit your Subject line so it is more specific<br class="">than "Re: Contents of fieldtrip digest..."<br class=""><br class=""><br class="">Today's Topics:<br class=""><br class=""> 1. Re: ft_channelrepair ignoring missing channels, and<br class=""> destroying grad info on elekta data (Schoffelen, J.M. (Jan Mathijs))<br class=""> 2. Re: ft_channelrepair ignoring missing channels, and<br class=""> destroying grad info on elekta data (Stephen Whitmarsh)<br class=""> 3. Permutation test for experiment with more than 2 conditions?<br class=""> (Sebastian Sauppe)<br class=""><br class=""><br class="">----------------------------------------------------------------------<br class=""><br class="">Message: 1<br class="">Date: Sat, 6 Apr 2019 11:24:30 +0000<br class="">From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen@donders.ru.nl><br class="">To: FieldTrip discussion list <fieldtrip@science.ru.nl><br class="">Subject: Re: [FieldTrip] ft_channelrepair ignoring missing channels,<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>and destroying grad info on elekta data<br class="">Message-ID: <3927E5EB-DA20-485A-AB8F-C13FCBA22EDF@donders.ru.nl><br class="">Content-Type: text/plain; charset="utf-8"<br class=""><br class="">Hi Craig,<br class="">There are a few open bugs about this on bugzilla.fieldtriptoolbox.org<http://bugzilla.fieldtriptoolbox.org> (2331 and 2404). We are moving away from bugzilla (and try to switch more to github issues), but the the currently open ones still contain some knowledge and history that’s worth to be looked into. Moreover, their resolution might be documented there as well.<br class="">I am not sure whether your old esi-e-mailaddress still works, that’s the one with which you are subscribed to bugzilla, but if not, I suggest that you update your e-mailaddress, so that you can check what has been documented regarding the issue you raise. Subsequently, you can work with us towards a solution, which eventually will end up as a pull request on the github repo.<br class=""><br class="">As a side note, I am wondering why you’d want to use ft_channelrepair on MEG data. I could think of the functionality being useful occasionally in EEG, but not in MEG.<br class=""><br class="">Best wishes,<br class=""><br class="">Jan-Mathijs<br class=""><br class=""><br class="">On 5 Apr 2019, at 19:05, Craig Richter <craiggrichter@gmail.com<mailto:craiggrichter@gmail.com>> wrote:<br class=""><br class="">Hey FTers,<br class=""><br class="">It appears that when a data structure with missing channels is entered into ft_channelrepair, the function is using the input data to determine the sens structure. Since the data is missing channels, the sens structure is also missing these channels, and no interpolation occurs, but no errors are thrown. It states that it was successful. The work-around is to provide a cfg.layout, or cfg.grad to ft_channelrepair, such that ft_fetch_sens does not depend on the input data and returns with a full sensor array, but in this case, the grad info in the data is lost. This appears to be a bug, though http://www.fieldtriptoolbox.org/example/fixing_a_missing_sensor/ would indicate this is the intended behaviour. Perhaps an error, or warning message should be generated. Also, the grad info is largely lost after interpolation except for chanpos and chanori. Is there no way to interpolate all the grad info, such that it is not lost (i.e. tra, and the coil data)?<br class=""><br class="">Any suggestions would be great!<br class=""><br class="">Thanks!<br class=""><br class="">C.<br class=""><br class="">Best,<br class=""><br class="">C.<br class="">_______________________________________________<br class="">fieldtrip mailing list<br class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">https://doi.org/10.1371/journal.pcbi.1002202<br class=""><br class="">-------------- next part --------------<br class="">An HTML attachment was scrubbed...<br class="">URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190406/60c4a33f/attachment.html><br class=""><br class="">------------------------------<br class=""><br class="">Message: 2<br class="">Date: Sat, 6 Apr 2019 14:24:00 +0200<br class="">From: Stephen Whitmarsh <stephen.whitmarsh@gmail.com><br class="">To: FieldTrip users <fieldtrip@science.ru.nl><br class="">Subject: Re: [FieldTrip] ft_channelrepair ignoring missing channels,<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>and destroying grad info on elekta data<br class="">Message-ID:<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><CAFrxm=xhJWskvYBKX5PDxJFyjNvEDH610kayu7ok3zS7ThxW5g@mail.gmail.com><br class="">Content-Type: text/plain; charset="utf-8"<br class=""><br class="">Hi Craig,<br class=""><br class="">If im not mistaken, maxfilter can repair channels.<br class=""><br class="">Cheers,<br class="">stephen<br class=""><br class=""><br class="">On Sat, 6 Apr 2019, 13:32 Schoffelen, J.M. (Jan Mathijs), <<br class="">jan.schoffelen@donders.ru.nl> wrote:<br class=""><br class=""><blockquote type="cite" class="">Hi Craig,<br class="">There are a few open bugs about this on bugzilla.fieldtriptoolbox.org (2331<br class="">and 2404). We are moving away from bugzilla (and try to switch more to<br class="">github issues), but the the currently open ones still contain some<br class="">knowledge and history that’s worth to be looked into. Moreover, their<br class="">resolution might be documented there as well.<br class="">I am not sure whether your old esi-e-mailaddress still works, that’s the<br class="">one with which you are subscribed to bugzilla, but if not, I suggest that<br class="">you update your e-mailaddress, so that you can check what has been<br class="">documented regarding the issue you raise. Subsequently, you can work with<br class="">us towards a solution, which eventually will end up as a pull request on<br class="">the github repo.<br class=""><br class="">As a side note, I am wondering why you’d want to use ft_channelrepair on<br class="">MEG data. I could think of the functionality being useful occasionally in<br class="">EEG, but not in MEG.<br class=""><br class="">Best wishes,<br class=""><br class="">Jan-Mathijs<br class=""><br class=""><br class="">On 5 Apr 2019, at 19:05, Craig Richter <craiggrichter@gmail.com> wrote:<br class=""><br class="">Hey FTers,<br class=""><br class="">It appears that when a data structure with missing channels is entered<br class="">into ft_channelrepair, the function is using the input data to determine<br class="">the sens structure. Since the data is missing channels, the sens structure<br class="">is also missing these channels, and no interpolation occurs, but no errors<br class="">are thrown. It states that it was successful. The work-around is to provide<br class="">a cfg.layout, or cfg.grad to ft_channelrepair, such that ft_fetch_sens does<br class="">not depend on the input data and returns with a full sensor array, but in<br class="">this case, the grad info in the data is lost. This appears to be a bug,<br class="">though http://www.fieldtriptoolbox.org/example/fixing_a_missing_sensor/<br class="">would indicate this is the intended behaviour. Perhaps an error, or warning<br class="">message should be generated. Also, the grad info is largely lost after<br class="">interpolation except for chanpos and chanori. Is there no way to<br class="">interpolate all the grad info, such that it is not lost (i.e. tra, and the<br class="">coil data)?<br class=""><br class="">Any suggestions would be great!<br class=""><br class="">Thanks!<br class=""><br class="">C.<br class=""><br class="">Best,<br class=""><br class="">C.<br class="">_______________________________________________<br class="">fieldtrip mailing list<br class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">https://doi.org/10.1371/journal.pcbi.1002202<br class=""><br class=""><br class="">_______________________________________________<br class="">fieldtrip mailing list<br class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">https://doi.org/10.1371/journal.pcbi.1002202<br class=""><br class=""></blockquote>-------------- next part --------------<br class="">An HTML attachment was scrubbed...<br class="">URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190406/de39a50c/attachment.html><br class=""><br class="">------------------------------<br class=""><br class="">Message: 3<br class="">Date: Sat, 6 Apr 2019 22:49:48 +0200<br class="">From: Sebastian Sauppe <sauppe.s@gmail.com><br class="">To: fieldtrip@science.ru.nl<br class="">Subject: [FieldTrip] Permutation test for experiment with more than 2<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>conditions?<br class="">Message-ID: <9732D7D9-C708-47BD-97EC-3D6CC53B0247@gmail.com><br class="">Content-Type: text/plain; charset="utf-8"<br class=""><br class="">Dear FieldTrip list members,<br class=""><br class="">What is the standard/recommended procedure if one wants to apply cluster based permutation tests to an experiment that has more than two conditions, e.g. with a 2x2 design. Is there a way to do this within ft_freqstatistics or would it be better to compare the different combinations of conditions in separate tests?<br class=""><br class="">Regards,<br class="">Sebastian<br class=""><br class="">-----------<br class="">Dr. Sebastian Sauppe<br class="">Department of Comparative Linguistics, University of Zurich<br class="">Homepage: https://sites.google.com/site/sauppes/ <https://sites.google.com/site/sauppes/><br class="">Twitter: @SebastianSauppe <https://twitter.com/SebastianSauppe><br class="">Google Scholar Citations: https://scholar.google.de/citations?user=wEtciKQAAAAJ <https://scholar.google.de/citations?user=wEtciKQAAAAJ> <br class="">ResearchGate: http://www.researchgate.net/profile/Sebastian_Sauppe <http://www.researchgate.net/profile/Sebastian_Sauppe><br class="">ORCID ID: http://orcid.org/0000-0001-8670-8197 <http://orcid.org/0000-0001-8670-8197><br class="">-------------- next part --------------<br class="">An HTML attachment was scrubbed...<br class="">URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190406/bb514602/attachment.html><br class=""><br class="">------------------------------<br class=""><br class="">Subject: Digest Footer<br class=""><br class="">_______________________________________________<br class="">fieldtrip mailing list<br class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">_______________________________________________<br class="">fieldtrip mailing list<br class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br class="">https://doi.org/10.1371/journal.pcbi.1002202<br class=""><br class=""><br class="">------------------------------<br class=""><br class="">End of fieldtrip Digest, Vol 101, Issue 6<br class="">*****************************************<br class=""></div></div></blockquote></div><br class=""></div></body></html>