using coil/isotrack information for sourceanalysis (neuromag data)

Laurence Hunt lhunt at FMRIB.OX.AC.UK
Wed Nov 18 14:40:14 CET 2009

Dear Hanneke,

The information stored in dig can indeed be read into fieldtrip; this
is done by read_headshape, which reads in all the points and
classifies them as fiducial (i.e. nasion/LPA/RPA), stored in
shape.fid, or other, stored in shape.pnt. shape.pnt would therefore
include your HPI coils and additional digitised points (and any
digitised EEG sensor locations if you collected EEG also).

As you're probably aware, there are two registrations that need to
take place - the first is the registration of coil locations to sensor
locations, and the second is the registration of the subject's MR scan
to the coil locations/fiducials. The first is done at the time of
recording (i.e. it is HPI); the sensors are by default read into
fieldtrip using the same co-ordinates as the coils/digitised points
(i.e. head coordinates rather than sensor coordinates, done by
mne2grad in read_header). The second is done by fieldtrip, and is the
registration of coil locations to the MR scan. This means that you
wouldn't be able to improve the registration of coils etc. to the
sensors (this registration has been done already by the HPI), but what
you might be able to do is to use the additional points to improve the
registration of the coil locations to the subject's MR scan. Typically
they should be located on the scalp, and by minimising the mean
squared error of the distance between coil locations/other digitised
points and scalp you should be able to get a good registration.

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?

Hope this helps,

Laurence Hunt, DPhil Student
  Centre for Functional MRI of the Brain (FMRIB),
University of Oxford
lhunt at
Phone: (+44)1865-(2)22738

On 18 Nov 2009, at 12:38, Hanneke Van Dijk wrote:

> Dear all,
> In my group we have a question regarding the use of the coil
> locations and/ or isotrack data to do source analysis. We are doing
> data analysis using FT and the MNE toolbox, on a dataset recorded
> with a Neuromag122 system.
> The four coils were placed in different locations then in the CTF
> system, which uses the anatomical landmarks (left ear, right ear and
> nasion). Here we placed the coils on the scalp; two approximately
> above the eyes and two behind the ears. We digitized the locations
> of the coils using the polhemus, togheter with the anatomical
> landmarks and some more points. We would very much like to know HOW
> and WHERE fieldtrip uses the coil-location information and if it is
> possible to use the polhemus data as well, to place the head at the
> correct location within the helmet and to do sourceanalysis.
> I noticed allready that when reading the fiff file with
> 'fiff_read_meas_info' (MNE) there is a field called .dig which seems
> to contain the coordinates of digitized locations. I have no idea
> though how to integrate this information into the data so fieldtrip
> can use it.
> Thanks in advance for any information,
> Hanneke van Dijk
> Institute for Clinical Neuroscience and Medical Psychology,
> Heinrich Heine Universitaet, Duesseldorf.
> ----------------------------------
> 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.

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
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