example_spm_render.m

% small script to show some basic way to render volume data on surfaces using SPM

clear
close all
clc

% which surface to use
% uses one of the default SPM surfaces but it should be doable to create you own
% from the results of a segmentation or from some freesurfer output to have
% a better group template
gii = fullfile(spm('dir'), 'canonical', 'cortex_5124.surf.gii');

con = '/home/remi/Downloads/AV-att/spm_0001.nidm/Contrast.nii';
tstat = '/home/remi/Downloads/AV-att/spm_0001.nidm/TStatistic.nii';

%% project the data of 2 volumes on the surface at once
% can be used for up to 3 images
% will be prompted for which color to use
spm_render(char({con;tstat}),NaN,gii)


%% project the data of 1 volumes on the surface 
% this one shows a couple more things from the SPM machinery you can use to
% script figure making

% open the gifti surface data file
M =  gifti(gii);

% inflate the surface
M2 = spm_mesh_inflate(M, 10);

% display the surface
H = spm_mesh_render(M2);

% sample the volume data only on the vertices (only on the surface)
% taken from spm_mesh_project
V = M.vertices;
P = zeros(1,size(V,1));
hdr      = spm_vol(con);
vol      = spm_read_vols(hdr);
Y = vol;
mat    = hdr.mat;

XYZ = double(inv(mat)*[V';ones(1,size(V,1))]);
P = spm_sample_vol(Y,XYZ(1,:),XYZ(2,:),XYZ(3,:),0);

AX = spm_mesh_render('Overlay', H, P)


%% thresholding
% in case you want to show beta values that only have t value superior to a
% certain value
t_val = spm_read_vols(spm_vol(tstat));
Y = vol;
% Y(t_val>1) = NaN;
Y(t_val<0.5) = NaN;

P = spm_sample_vol(Y,XYZ(1,:),XYZ(2,:),XYZ(3,:),0);

AX = spm_mesh_render('Overlay', H, P);