MNI aligned grids, mris and segmentation

Robert Oostenveld r.oostenveld at FCDONDERS.RU.NL
Wed Mar 21 13:37:39 CET 2007

On 20 Mar 2007, at 19:10, Sameer Walawalkar wrote:
> I am using Neuromag 306 data. Or the MRIs, I have already used MNE
> to generate bem head model meshes stored in files of kind
> <something>_bem_sol.fif, but which fieldtrip program do I use to
> extract this (the info is for ctf and I could not find an intuitive
> or obvious extension to my case).
> Can I simply proceed as

You can use neuromag BEM models, but that requires a licensed copy of
the meg-calc toolbox (which contans some mex files that are then
called by fieldtrip).

> bem_head = appropriate-field-trip-function(<something>_bem_sol.fif);
> hdr = read_fcdc_header(datafile.fif);
> cfg = [];
> cfg.grad = hdr.grad;

instead of cfg.grad please specify cfg.gradfile='datafile.fif', since
has to be interpreted by the neuromag mex files.

> cfg.vol = bem_head;

instead of reading the model with appropriate-field-trip-function()
you should specify the file that contains the model. That is done
with cfg.hdmfile. The neuromag mex file will then "initialize" with
the model in the fif file.

> cfg.resolution = 1;
> grid_bem = prepare_leadfield(cfg);

Then the remainder should in principle work. I have not been able to
test it exhaustivelym since I do not have a license for the neuromag
meg-calc toolbox.

> Also am not sure how to extract head shape which is needed for
> plotting headmodel. Is it shimply the HPI coils information ?

The head shape is the triangulated boundary. That boundary will be
read from the fif file at the appropriate time (e.g. in
headmodelplot). Actually, the initialization of the neuromag mex
files and reading of the triangulation is done in private/
prepare_vol_sens. I suggest you look in that function and search for

hope this helps,

PS you can also use other head models, such as single and multiple
spheres and a analytic realistic single-shell model. Those are all
implemneted in plain Matlab.

More information about the fieldtrip mailing list