Skip to content

Latest commit

 

History

History
96 lines (71 loc) · 3.15 KB

coregistration_quality_control.md

File metadata and controls

96 lines (71 loc) · 3.15 KB
Raw
title tags
Check the quality of the anatomical coregistration
example
source
mri
plotting

Check the quality of the anatomical coregistration

The following code makes a number of figures that can be used as quality control for the procedure to coregister the MRI with the MEG.

{% include markup/danger %} Please note that this is an example where the coregistration was not completely correct. The head is tilted to the left. {% include markup/end %}

%% load the required data

load headmodel_mri.mat
load headshapeMEG.mat % from the fiff file
load mri_resliced.mat % resliced
load mri_segmented.mat
load sens.mat

%% figure 1

figure
ft_plot_sens(sens, 'unit', 'mm')
ft_plot_headshape(headshapeMEG, 'unit', 'mm')
ft_plot_headmodel(headmodel_mri, 'unit', 'mm')
ft_plot_axes([], 'unit', 'mm');

{% include image src="/assets/img/example/coregistration_quality_control/coreg_qc_fig1.png" width="400" %}

%% figure 2, MRI anatomy and brain segmentation

cfg = [];
cfg.anaparameter = 'anatomy';
cfg.funparameter = 'brain';
cfg.location = [0 0 60];
ft_sourceplot(cfg, mri_segmented)

{% include image src="/assets/img/example/coregistration_quality_control/coreg_qc_fig2.png" width="400" %}

%% figure 3 and 4, MRI anatomy and headmodel

location = [0 0 60];
figure
ft_plot_ortho(mri_resliced.anatomy, 'transform', mri_resliced.transform, 'location', location, 'intersectmesh', headmodel_mri.bnd)

figure
ft_plot_montage(mri_resliced.anatomy, 'transform', mri_resliced.transform, 'intersectmesh', headmodel_mri.bnd)

{% include image src="/assets/img/example/coregistration_quality_control/coreg_qc_fig3.png" width="400" %} {% include image src="/assets/img/example/coregistration_quality_control/coreg_qc_fig4.png" width="400" %}

%% figure 5, MRI scalp surface and polhemus headshape

cfg = [];
cfg.tissue = 'scalp';
cfg.method = 'isosurface';
cfg.numvertices = 10000;
scalp = ft_prepare_mesh(cfg, mri_segmented);

figure
ft_plot_mesh(scalp, 'facecolor', 'skin')
lighting phong
camlight left
camlight right
material dull
alpha 0.5
ft_plot_headshape(headshapeMEG, 'vertexcolor', 'k');

{% include image src="/assets/img/example/coregistration_quality_control/coreg_qc_fig5.png" width="400" %}

%% figure 6, MRI and anatomical landmarks

figure
for i=1:3
  subplot(2,2,i)
  title(headshapeMEG.fid.label{i});
  location = headshapeMEG.fid.pos(i,:);
  ft_plot_ortho(mri_resliced.anatomy, 'transform', mri_resliced.transform, 'style', 'intersect', 'location', location, 'plotmarker', location, 'markersize', 5, 'markercolor', 'y')
end

{% include image src="/assets/img/example/coregistration_quality_control/coreg_qc_fig6.png" width="400" %}

%% figure 7, MRI scalp surface and anatomical landmarks

figure
ft_plot_mesh(scalp, 'facecolor', 'skin')
lighting phong
camlight left
camlight right
material dull
alpha 0.3
ft_plot_mesh(headshapeMEG.fid, 'vertexcolor', 'k', 'vertexsize', 10);

{% include image src="/assets/img/example/coregistration_quality_control/coreg_qc_fig7.png" width="400" %}