[FieldTrip] Fwd: How to understand the channel location of ctf275 MEG data

Schoffelen, J.M. (Jan Mathijs) janmathijs.schoffelen at donders.ru.nl
Fri Aug 5 16:48:11 CEST 2022

Begin forwarded message:

I am building head models for each subject hence channel location does affect the source reconstruction. Because these data were collected by another lab 10 years ago. Hence I guess I cannot know what happened to some problematic data. Now I just remove subjects with obviously wrong head models from my analysis. I know SPM can fix the channel location if continuous head location data was collected. I have tried it but the head model did not get better. May I ask if you know any other toolbox or standard pipeline for adjusting channel location for head model inversion? Many thanks.


Li Zhi

On Fri, 5 Aug 2022 at 10:02, Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen at donders.ru.nl<mailto:janmathijs.schoffelen at donders.ru.nl>> wrote:
As long as you stick to a sensor level analysis, there is no need to ‘fix’ it. Of course the subject can only be included if you are sure that they were more or less normally positioned in the MEG. For this you would need to check your lab notebook (or ask the person who has collected the data).

Best wishes,

On 4 Aug 2022, at 21:17, Zhi Li <lizhi.psych at gmail.com<mailto:lizhi.psych at gmail.com>> wrote:

Hi Jan-Mathijs,

Thanks for your kind suggestion. The x-coordinates of channels of the third subject are much bigger than others and I do not know why. May I ask if there is any method to fix problematic channel location after data collection? Many thanks.


Li Zhi

On Thu, 4 Aug 2022 at 14:31, Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:
Hi Li Zhi,

Sensor coordinates are registered to a coordinate system that is determined on a per measurement basis. This coordinate system is determined based on how the head positioning coils have been positioned on the participant’s head (typically on the nasion, and on the left/right ear). The positions of the sensors then also depend on how the participant was positioned in the MEG device, which may cause slight (but not too big) differences across participants. The first two sets of numbers that you report make sense to me, the third set of numbers (with an x-coordinate of 20 cm(?)) seems off to me. This FAQ https://www.fieldtriptoolbox.org/faq/coordsys/<https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/faq/coordsys/__;!!HJOPV4FYYWzcc1jazlU!-Gw0xFiULIb9yE5AE08dtMVSFJQLNg6wMNyM-WnW_sGtfEFA5ihWeZlv__fO5h967GsT-WZm59BX8q_dCf3aUyWT_Bu6196lcb4$> explains a bit more about coordinate systems.

In general, for sensor level analyses no standardisation is done. I would double check your third subject though, because something might have gone wrong with the head localization procedure.

Best wishes,

> On 14 Jul 2022, at 18:41, Zhi Li via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:
> Hi,
> I am new to MEG data and have no experience in collecting them. When I processed the ctf275 MEG data, I found that the channel location in hdr.grad.chanpos were not the same across subjects. For example, the Cartesian coordinates of MLC11 from the data of 3 subjects were [7.96, 1.67, 13.94], [8.9, 1.1, 13.68] and [20.04, -0.03, 14.33] respectively. Hence both the 3D channel location and their 2D projections are different across subjects. May I ask how these Cartesian coordinates were calculated and should we standardize them before data processing, i.e., make the channel location the same across subjects? Any suggestions would be much appreciated.
> Best,
> Li Zhi
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