Fieldtrip: KIT to fieldtrip

Lead author: Osama Abdullah osama.abdullah@nyu.edu

This notebook is to be run in MATLAB, it facilitates the importing of the raw KIT files, laser scan files and MRI anatomical data into fieldtrip for data processing purposes. The oddball experiment data is used as an example.

Specify the as BOX_DIR an environment variable pointing towards the BOX://MEG/Data folder and set the variable in your script.

% MRI-MEG KIT coregisteration
clear all
close all
clc

Ensure the environment variable is properly set to the MEG Data folder

BOX_DIR = getenv('BOX_DIR');
disp(BOX_DIR)

C:\Users\hz3752\Box\MEG\Data

Specify the needed files, a T1w MRI scan, MEG data .con file, laser surface scan of the head .txt, stylus points from laser scan .txt, atleast two HPI KIT coils .mrk files

% It is important that you use T1.mgz instead of orig.mgz as T1.mgz is normalized to [255,255,255] dimension
mrifile     = fullfile([BOX_DIR,'oddball\sub-03\anat\sub-003\sub-003\mri\T1.mgz']);
confile    = fullfile([BOX_DIR,'oddball\sub-03\meg-kit\sub-03-raw-kit.con']);
laser_surf = fullfile([BOX_DIR,'oddball\sub-03\meg-kit\sub-03-basic-surface.txt']);
laser_points = [BOX_DIR, 'oddball\sub-03\meg-kit\sub-03-stylus.txt'];
mrkfile1 = [BOX_DIR,'oddball\sub-03\meg-kit\240524-1.mrk'];
mrkfile2 = [BOX_DIR, 'oddball\sub-03\meg-kit\240524-2.mrk'];

%% Read Laser headshape (points and fudicials)
lasershape   = read_head_shape_laser(laser_surf,laser_points);
lasershape   = ft_convert_units(lasershape, 'cm');
laser2ctf = ft_headcoordinates(lasershape.fid.pos(1,:),lasershape.fid.pos(4,:),lasershape.fid.pos(5,:),'ctf');
lasershape = ft_transform_geometry(laser2ctf, lasershape)
ft_determine_coordsys(lasershape, 'interactive', 'no')

% Deface the laser mesh under a certain plan (change the 140) Define the configuration for ft_defacemesh
planecut = 140;
cfg = [];
cfg.method    = 'plane';       % Use a plane for exclusion
cfg.translate = [0 planecut 0]; % A point on the plane (adjust z_value as needed)
cfg.rotate    = [0 0 0];       % Rotation vector, modify if the plane is not axis-aligned
cfg.selection = 'outside';     % Remove points below the plane
% Apply ft_defacemesh to remove points below the plane
mesh = ft_defacemesh(cfg, lasershape);
% Plot the resulting mesh to check the results
ft_plot_mesh(mesh);
lasershape = mesh

%% read mri and mri-headshape
mri = ft_read_mri(mrifile); % read mri file
mri = ft_convert_units(mri, 'cm'); %make sure units cm
% mri = ft_determine_coordsys(mri, 'interactive', 'no');
cfg             = [];
cfg.method      = 'interactive';
cfg.coordsys    = 'ctf'; %use CTF coordinates (pos x toward nose, +y to left)
mri_init = ft_volumerealign(cfg,mri)
ft_determine_coordsys(mri_init, 'interactive', 'no'); % sanity check, should be CTF

%% Align MEG Dewar to Laser scan Head model
% now we want to align the 3 markers in the *.con file with the 3 markers
% in the lasershape, where 1:5 markers match to the 4:9 lasershape
% fiducials
mrk1 = ft_read_headshape(mrkfile1);
mrk1 = ft_convert_units(mrk1, lasershape.unit);
mrk2 = ft_read_headshape(mrkfile2);
mrk2 = ft_convert_units(mrk2, lasershape.unit);
mrka = mrk1;
mrka.fid.pos = (mrk1.fid.pos+mrk2.fid.pos)/2;
p1 = mrka.fid.pos(1:5,:);
p2 = lasershape.fid.pos;
t1 = ft_headcoordinates(p1(1,:), p1(2,:), p1(3,:), 'ctf');%J
t2 = ft_headcoordinates(p2(6,:), p2(4,:), p2(5,:), 'ctf');%J
% t1 = ft_headcoordinates(p1(1,:), p1(2,:), p1(3,:), 'ctf');
% t2 = ft_headcoordinates(p2(1,:), p2(4,:), p2(5,:), 'ctf');
transform_mrk2laser = t2\t1;
% p1t = ft_warp_apply(transform_mrk2laser, p1)
grad = ft_read_sens(confile,'senstype','meg');
grad = ft_transform_geometry(transform_mrk2laser, grad);

%% align MRI and Laser
cfg = []
cfg.method = 'headshape';
cfg.headshape = lasershape;
cfg.headshape.interactive = 'no'
cfg.headshape.icp = 'yes'
mri_aligned = ft_volumerealign(cfg,mri_init)
% ft_determine_coordsys(mri_aligned,'interactive', 'no')
%% segmentation MRI
cfg           = [];
cfg.output    = {'brain', 'skull', 'scalp'};
segmentedmri  = ft_volumesegment(cfg, mri_aligned);
save segmentedmri segmentedmri
cfg = [];
cfg.method='singleshell';
mriskullmodel = ft_prepare_headmodel(cfg, segmentedmri);
cfg = [];
cfg.tissue      = {'brain', 'skull', 'scalp'};
cfg.numvertices = [3000 2000 1000];
mesh = ft_prepare_mesh(cfg, segmentedmri);
% ft_plot_mesh(mesh(3), 'facecolor', 'none'); % scalp
%%
cfg = [];
%   cfg.elec              = structure, see FT_READ_SENS
   cfg.grad              = grad;%structure, see FT_READ_SENS
%   cfg.opto              = structure, see FT_READ_SENS
  cfg.headshape         = mesh(3)%structure, see FT_READ_HEADSHAPE
  cfg.headmodel         = mriskullmodel% structure, see FT_PREPARE_HEADMODEL and FT_READ_HEADMODEL
%   cfg.sourcemodel       = structure, see FT_PREPARE_SOURCEMODEL
%   cfg.dipole            = structure, see FT_DIPOLEFITTING
  cfg.mri               = mri_aligned;
  cfg.mesh              = lasershape;
  cfg.axes              = 'yes'
ft_geometryplot(cfg)