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

Vladimir Litvak litvak.vladimir at gmail.com
Fri Aug 5 18:06:40 CEST 2022

Hi Jan-Mathijs,

Your description of what that SPM function does is 100% correct. It's also
robust to occasional poor continuous head tracking. I'm not sure if the
12cm shift is in the same example I saw but there the problem was an
incorrectly recorded fiducial. That could indeed be remedied by that SPM


On Fri, Aug 5, 2022 at 4:27 PM Schoffelen, J.M. (Jan Mathijs) via fieldtrip
<fieldtrip at science.ru.nl> wrote:

> Hi Li Zhi,
> I don’t understand why you think that something can (or needs to) be fixed.
> You say "I am building head models for each subject hence channel location
> does affect the source reconstruction”. I don’t understand this. A
> headmodel is constructed from anatomical data (ideally), which is
> independent of the functional MEG data and the sensor description.
> In general, a source reconstruction will be only valid if the sensor
> positions are expressed in the same coordinate system as the headmodel.
> Once this is ensured (and as a side note: for what it’s worth the origin of
> the coordinate system can be defined on the moon, and the distance units in
> lightyears, as long as its consistent), the source reconstruction will be
> correct. Whether it’s a good result, depends on how the subject was
> positioned in the MEG (e.g. far away from the sensors), but not on whether
> or not the subject was e.g. in sitting or supine position, or even facing
> backward. I don’t understand what you mean with SPM ‘fixing’ the channel
> locations, at least not how this will address the problem you have been
> sketching so far. If anything (but correct me if I’m wrong) the SPM
> procedure will adjust the sensor positions as they will be used for the
> source reconstruction to reflect the average position of the subject
> throughout the measurement, rather than the initial head position that was
> determined by the localization procedure just prior to starting data
> acquisition. If there’s continuous head position information in the data
> you are working with, you may want to check those traces for the outlier
> subject(s). I doubt whether this will explain away the 12 cm anterior shift
> (because there is not sufficient space in the MEG to move the head over
> such a distance).
> Best wishes,
> Jan-Mathijs
> On 5 Aug 2022, at 16:48, Schoffelen, J.M. (Jan Mathijs) <
> janmathijs.schoffelen at donders.ru.nl> wrote:
> 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.
> Best,
> Li Zhi
> On Fri, 5 Aug 2022 at 10:02, Schoffelen, J.M. (Jan Mathijs) <
> 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,
>> Jan-Mathijs
>> On 4 Aug 2022, at 21:17, Zhi Li <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.
>> Best,
>> Li Zhi
>> On Thu, 4 Aug 2022 at 14:31, Schoffelen, J.M. (Jan Mathijs) via fieldtrip
>> <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,
>>> Jan-Mathijs
>>> > On 14 Jul 2022, at 18:41, Zhi Li via fieldtrip <
>>> 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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