[FieldTrip] fieldtrip Digest, Vol 101, Issue 6
Craig Richter
craiggrichter at gmail.com
Sun Apr 7 14:32:22 CEST 2019
Thanks Stephen and Jan-Mathijs,
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:
http://imaging.mrc-cbu.cam.ac.uk/meg/InterpolateData <http://imaging.mrc-cbu.cam.ac.uk/meg/InterpolateData>
My ESI address it still working. I got the bug CC.
Best,
C.
> On 7. Apr 2019, at 12:00, fieldtrip-request at science.ru.nl wrote:
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> Today's Topics:
>
> 1. Re: ft_channelrepair ignoring missing channels, and
> destroying grad info on elekta data (Schoffelen, J.M. (Jan Mathijs))
> 2. Re: ft_channelrepair ignoring missing channels, and
> destroying grad info on elekta data (Stephen Whitmarsh)
> 3. Permutation test for experiment with more than 2 conditions?
> (Sebastian Sauppe)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 6 Apr 2019 11:24:30 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] ft_channelrepair ignoring missing channels,
> and destroying grad info on elekta data
> Message-ID: <3927E5EB-DA20-485A-AB8F-C13FCBA22EDF at donders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Craig,
> 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.
> 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.
>
> 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.
>
> Best wishes,
>
> Jan-Mathijs
>
>
> On 5 Apr 2019, at 19:05, Craig Richter <craiggrichter at gmail.com<mailto:craiggrichter at gmail.com>> wrote:
>
> Hey FTers,
>
> 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)?
>
> Any suggestions would be great!
>
> Thanks!
>
> C.
>
> Best,
>
> C.
> _______________________________________________
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> https://doi.org/10.1371/journal.pcbi.1002202
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> ------------------------------
>
> Message: 2
> Date: Sat, 6 Apr 2019 14:24:00 +0200
> From: Stephen Whitmarsh <stephen.whitmarsh at gmail.com>
> To: FieldTrip users <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] ft_channelrepair ignoring missing channels,
> and destroying grad info on elekta data
> Message-ID:
> <CAFrxm=xhJWskvYBKX5PDxJFyjNvEDH610kayu7ok3zS7ThxW5g at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Craig,
>
> If im not mistaken, maxfilter can repair channels.
>
> Cheers,
> stephen
>
>
> On Sat, 6 Apr 2019, 13:32 Schoffelen, J.M. (Jan Mathijs), <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Hi Craig,
>> There are a few open bugs about this on 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.
>> 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.
>>
>> 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.
>>
>> Best wishes,
>>
>> Jan-Mathijs
>>
>>
>> On 5 Apr 2019, at 19:05, Craig Richter <craiggrichter at gmail.com> wrote:
>>
>> Hey FTers,
>>
>> 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)?
>>
>> Any suggestions would be great!
>>
>> Thanks!
>>
>> C.
>>
>> Best,
>>
>> C.
>> _______________________________________________
>> fieldtrip mailing list
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> https://doi.org/10.1371/journal.pcbi.1002202
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> https://doi.org/10.1371/journal.pcbi.1002202
>>
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> ------------------------------
>
> Message: 3
> Date: Sat, 6 Apr 2019 22:49:48 +0200
> From: Sebastian Sauppe <sauppe.s at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Permutation test for experiment with more than 2
> conditions?
> Message-ID: <9732D7D9-C708-47BD-97EC-3D6CC53B0247 at gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear FieldTrip list members,
>
> 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?
>
> Regards,
> Sebastian
>
> -----------
> Dr. Sebastian Sauppe
> Department of Comparative Linguistics, University of Zurich
> Homepage: https://sites.google.com/site/sauppes/ <https://sites.google.com/site/sauppes/>
> Twitter: @SebastianSauppe <https://twitter.com/SebastianSauppe>
> Google Scholar Citations: https://scholar.google.de/citations?user=wEtciKQAAAAJ <https://scholar.google.de/citations?user=wEtciKQAAAAJ>
> ResearchGate: http://www.researchgate.net/profile/Sebastian_Sauppe <http://www.researchgate.net/profile/Sebastian_Sauppe>
> ORCID ID: http://orcid.org/0000-0001-8670-8197 <http://orcid.org/0000-0001-8670-8197>
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