using coil/isotrack information for sourceanalysis (neuromag data)

Robert Oostenveld r.oostenveld at FCDONDERS.RU.NL
Mon Nov 23 09:00:05 CET 2009

Hi Hanneke, 

On 18 Nov 2009, at 14:40, Laurence Hunt wrote:

> ...
> Unfortunately I'm not quite sure how or whether fieldtrip does this; I'm afraid I use fieldtrip mainly to read the data into SPM (which does allow you to use these additional points to aid registration to the subject's scalp surface). But I imagine fieldtrip is able to do this also, and perhaps someone who knows more about fieldtrip could explain how to use the information in read_headshape to achieve this?

Laurences description of the two steps are correct. First the position of the MEG sensors is expressed in a coordinate system relative to the fiducials, subseuqnelty the posiiton of the MRI has to be expressed in the same coordinate system.

For the MEG gradiometer coils fieldtripFT relies on the low-level reader (in this case in combination with mne2grad.m) to contain the position in the correct coordinate system. In the CTF case (as an example), the res4  file contains the coil posiitons both in head coorindates, but also in dewar coordinates. FieldTrip reads the coil positions in head coordinates and stores them in grad.pnt and grad.ori (orientation is also relevant here). 

The usual procedure for the MRI in the CTF case is to use MRIViewer to click on the fiducials and then store the mri file with the coordinate system re-defined according to the fiducials. The volumerealign.m function allows to do the same in fieldtrip in case you don't have vendor-specific software to assign the coordinate system.

What I'm not sure about is whether you want to represent the MEG coils and MRI relative to the localizer coils, or relative to the Nose/Ear fiducials. The first case is quite simple, because that only requires you to identify the localizer coils in the MRI. The second case is more tricky, because you then first have to specify the MEG coils and MRI in the localizer-coil coordinate system, compute the  transformation from localizer coil coordinate system to fiducial coordinate system, and then apply that transform to both MEG coil positions+orientations and to the MRI.

FT functions that pertain to this (but are normally low-level and not used by the end user) are headcoordinates, which allows you to compute the coordinate transformation matrix from A to B given three new points that describe coordinate system B, expressed in coordinate system A. The function forwinv/transform_sens can be used to apply the transformation to the sensors, The function warp_apply is used, and applying the transformation to the MRI is as simple as multiplying h, the output of headcoordinates with mri.tra, such that mri.tra = h*mri.tra.

Important is that you carefully check the alignment of the MRI with the sensors by plotting them combined in 3D. The functions plot_slice and plot_sens (both in plotting) can be used for that.

Hope this helps.

Robert Oostenveld, PhD
Senior Researcher
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
tel.: +31 (0)24 3619695
e-mail: r.oostenveld at
skype: r.oostenveld

The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also and
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the fieldtrip mailing list