cifti2nifti.m

function cifti2nifti(image)
% Beta version to covert cifti image into nifti
% This function should be extended to convert different cifti file types
% ATM only converts parcellations stored in the dlabel.nii file
% 
% Input: CIFTI image (dlabel)
%
% Output: NIFTI image in MNI space(2mm)
%_________________________________________________________________________
% Carlos Hernandez 2018
% Amended by Maedbh King (22/02/18). 

[dir,n]=spm_fileparts(image);
name=strsplit(n,'.');

% Read CIFTI
cii=ft_read_cifti(image);

if isfield(cii,'indexmax'),
    labels=cii.indexmax;
else % this includes cortical labels, which need to be removed
    labels=cii.x1; 
    cii.pos(cii.brainstructure==1 | cii.brainstructure==2,:,:)=[]; 
    labels(cii.brainstructure==1 | cii.brainstructure==2)=[]; 
end

numVox=size(labels,1);

% Conversion from mm to vox
for v=1:numVox,
    tmp=inv(cii.transform)*[cii.pos(v,:),1]'; 
    vox(v,:)=tmp'; 
end

% Write Labels
DATA=zeros(cii.dim);
for i=1:numVox,
    DATA(vox(i,1),vox(i,2),vox(i,3))=labels(i); 
end

% MNI 2mm data structure
V = struct('fname',[dir 'C2N_' name{1} '.nii'],... 
            'dim',cii.dim,...
            'dt',[4 0],...
            'mat',[-2 0 0 92;0 2 0 -128;0 0 2 -74;0 0 0 1],...
            'pinfo',[1;0;352],...
            'descrip','MNI_2mm');
V = spm_create_vol(V);
spm_write_vol(V,DATA);