co-ordinate

Robert Oostenveld r.oostenveld at FCDONDERS.RU.NL
Thu Nov 18 12:30:55 CET 2004


Hi Sreenivasan

On 18 Nov 2004, at 0:00, R. Sreenivasan wrote:

> Is there any function in Fieldtrip to translate the Freesurfer-RAS or
> Talairach co-ordinate system to the system that Fieldtrip uses? (e.g.
> giving
> the dipole position - cfg.grid.pos = [x y z] for source analysis)

Fieldtrip does not use it's own intrinsic coordinate system. Instead,
if you read in geometrical information from a CTF file (dataset or
mri), that geometrical information such as sensor positions or voxels
will be represented in Matlab memory in CTF coordinates. For other
types of input data (e.g. Neuromag MEG or SPM/analyze MRI's) the
coordinate system can be different. As the user it is your own
responsibility to ensure that coordinate systems of the different input
objects/datafiles match.

Of course it is possible to "convert from one to the other coordinate
system". But conceptually one does not convert the coordinate system,
instead the geometrical description of the data is converted: i.e. a [x
y z] point in one coordinate system is converted to [x' y' z'] in
another coordinate system.

Please have a look at
   http://www2.ru.nl/fcdonders/fieldtrip/faq.html#q4
   http://www2.ru.nl/fcdonders/fieldtrip/faq.html#q5
to see the Fieldtrip specific details. Furthermore, I suggest that you
have a look at
   http://bishopw.loni.ucla.edu/AIR5/homogenous.html
to get an understanding for the general concept of a "homogenous
coordinate transformation", which is used in Fieldtrip.

Basically the problem boils down to obtaining a mathematical
description of the coordinate transformation that relates your data (in
CTF coordinates I guess) to Freesurfer-RAS or Talairach coordinates. I
don't know what Freesurfer-RAS uses, but Talairach and CTF cannot be
linked easily together with this homogenous transformation. E.g. SPM
uses nonlinear spatial normalization to align an individual MRI to a
standard MRI. This SPM approach of spatially realigning or normalizing
volume data will become part of Fieldtrip in the future.

> The other question is related to extracting source single-trial data.
>
> Earlier You suggested that the source signal could be extracted by the
> following way: ([u,s,v]=svd(dipole.moment)) and  s*v produces 3
> components
> of source.  Instead can we compute from the dipole (3D) moment by
> sqrt(x^2+y^2+z^2) for each trial?

Yes, but that is the magnitude of the rotating dipole moment instead of
its strength along a specified direction (which you would gvet with the
svd trick). The magnitude is always positive, the strength along one
direction is both positive and negative. You can use whichever you
think best captures the activity at that particular location, but
personally I prefer the dipole moment amplitude along a specific
direction because of its more clear physical interpretation.

best regards,
Robert Oostenveld



More information about the fieldtrip mailing list