[FieldTrip] converting sensor coordinates to MNI coordinates

jan-mathijs schoffelen jan.schoffelen at donders.ru.nl
Wed Oct 31 14:12:57 CET 2012

Hi Frederic,

What is the question exactly? This is the first time that you mention the word 'MNI' so I am a bit puzzled what you're after (and with me perhaps the rest of us mortals as well, which could explain the lack of answers). 
What you refer to as 'sensor space' is a coordinate system that is defined based on the head of the participant, i.e. based on three anatomical landmarks: LPA, RPA, and Nasion.
The transformation to MNI-space is not straightforward because this is generally based on a non-linear warp. 
If you are happy with an approximation, then you could use ft_volumenormalise to extract the linear transformation from individual head space into +/- MNI-space. This coordinate system is defined based on three other anatomical landmarks: AC, PC and a point defining the positive z-axis.

You can do either of the following things:

-Take an individual MRI (that is coregistered to the individual's head, i.e. it has a transform that defines the head coordinate system correctly).
-Call ft_volumenormalise (with cfg.nonlinear = 'no')
-The output volume (let's call this variable normalise) contains a transformation matrix in normalise.cfg.final, that transforms from head space into 'MNI-space'.
-You can use warp_apply to transform between the different coordinate systems, using the transformation matrix (or its inverse) to toggle coordinates back and forth.

-Take an individual MRI.
-specify mri.transform = eye(4) (assuming that the MRI is 1mm isotropic).
-call ft_volumerealign twice with cfg.interactive = 'yes'.
-once you specify lpa, rpa and nasion interactively.
-once you specify ac, pc and a z-point interactively.
-these two calls result in two transformation matrices, the first defining how to interpret the MRI voxels in coordinate system 1, the other defining how to interpret the MRI voxels in coordinate system 2.
-I leave it as an exercise to you how to combine these to in order to toggle from one coordinate system to the other directly.

Good luck,

Jan-Mathijs Schoffelen

On Oct 30, 2012, at 5:58 PM, Frederic Roux wrote:

> Dear List members,
> this post is related to a question that I have
> been posting several times now, but for which
> I haven't found an answer yet.
> I have a set of coordinates [5,0,-1] which should
> correspond to a point in sensor space.
> Is it possible to compute the corresponding coordinates
> in MNI space using a transformation matrix or anything
> similar?
> Any help or suggestions would be highly appreciated.
> Fred
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

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