Difference between revisions of "FreeSurferToFieldTrip"
(add update bem coord sys function) |
(→In MATLAB: add some subsections) |
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= In MATLAB = | = In MATLAB = | ||
| + | == Load data == | ||
Read the Nifti | Read the Nifti | ||
| Line 34: | Line 35: | ||
plot_bem_surfs(bems); | plot_bem_surfs(bems); | ||
</pre> | </pre> | ||
| + | |||
| + | == To CTF coordinates == | ||
At this point, the T1 and BEM surfaces are in the same coord sys but FieldTrip doesn't know which sys this is, and more importantly, a registration is required with the sensors. | At this point, the T1 and BEM surfaces are in the same coord sys but FieldTrip doesn't know which sys this is, and more importantly, a registration is required with the sensors. | ||
| Line 47: | Line 50: | ||
<pre>bems = update_bems_coord_sys(bems, t1.transform/t1.transformorig);</pre> | <pre>bems = update_bems_coord_sys(bems, t1.transform/t1.transformorig);</pre> | ||
| + | |||
| + | Now verify again everything's aligned | ||
| + | |||
| + | <pre> | ||
| + | ft_determine_coordsys(t1, 'interactive', 'no') | ||
| + | hold on | ||
| + | plot_bem_surfs(bems); | ||
| + | </pre> | ||
| + | |||
| + | == building the FieldTrip head model == | ||
= Helper functions = | = Helper functions = | ||
Revision as of 16:16, 5 May 2015
The FreeSurfer software provides a good automatic segmentation of T1 images. It includes utilities to generate BEM surfaces that can be used to construct a head model for FieldTrip.
The following assumes you've run FreeSurfer on your T1.
Contents
Post-recon steps in the shell
Generate BEM surfaces (brain, inner/outer skull & outer skin)
SUBJECTS_DIR=~/mris-tms/fs SUBJECT=anattms_50 mne_watershed_bem
Convert T1 to nifti
mri_convert fs/anattms_50/mri/T1.mgz fs/anattms_50/mri/T1.mgz.nii
Obtain transform from T1 voxels to BEM surface space
mri_info --vox2raw-tkr fs/anattms_50/mri/T1.mgz > fs/anattms_50/transforms/t1-vox2ras-tkr.xfm
In MATLAB
Load data
Read the Nifti
t1 = ft_read_mri('fs/anattms_50/mri/T1.mgz.nii')
Read the BEM surfaces (this function is given below)
bems = read_bem_surfs('fs/', 'anattms_50');
Plot the two together
ft_determine_coordsys(t1, 'interactive', 'no') hold on plot_bem_surfs(bems);
To CTF coordinates
At this point, the T1 and BEM surfaces are in the same coord sys but FieldTrip doesn't know which sys this is, and more importantly, a registration is required with the sensors.
Identify fiducial points (however you like; I use a simple imagesc based function https://gist.github.com/maedoc/97f7d4d4e30c9123e748)
fids = gofish(t1); t1 = ft_volumerealign(fids, t1);
Now, the T1 has a CTF based coord system, but the BEM surfaces need to have their vertices updated (again, this is defined below):
bems = update_bems_coord_sys(bems, t1.transform/t1.transformorig);
Now verify again everything's aligned
ft_determine_coordsys(t1, 'interactive', 'no') hold on plot_bem_surfs(bems);
building the FieldTrip head model
Helper functions
BEM surfaces
update_bems_coord_sys
function bems = update_bems_coord_sys(bems, xfm)
surfs = {'brain', 'inner_skull', 'outer_skull', 'outer_skin'};
for i=1:length(surfs)
si = surfs{i};
v = bems.(si).vertices;
v = [v ones(size(v, 1), 1)];
v = v*xfm';
bems.(si).vertices = v(:, 1:3);
end
