img2imgcoords.m

%% transforms
% transform into fsl coordinates (CT)
fslpos = elec.elecpos;
fslpos(:,4) = 1;
fslpos = (img_ct.transform \ fslpos')';

if img_ct.hdr.x_r == 1
  fslpos(:,1) = img_ct.dim(1) - fslpos(:,1);
end

fslpos(:,1) = fslpos(:,1) * img_ct.hdr.xsize;
fslpos(:,2) = fslpos(:,2) * img_ct.hdr.ysize;
fslpos(:,3) = fslpos(:,3) * img_ct.hdr.zsize;

% apply affine
fslpos(:,4) = 1;
fslpos = (CTtoMRI_Affine * fslpos')';

% transform fsl coordinates (MR) to scanner
fslpos(:,4) = 1;
fslpos(:,1) = fslpos(:,1) ./ img_mri.hdr.xsize;
fslpos(:,2) = fslpos(:,2) ./ img_mri.hdr.ysize;
fslpos(:,3) = fslpos(:,3) ./ img_mri.hdr.zsize;

if img_mri.hdr.x_r == 1
  fslpos(:,1) = img_mri.dim(1) - fslpos(:,1);
end

mrimmpos = (img_mri.transform * fslpos')';