clear

% Change the path accordingly
cd('C:\Users\Konstantinos Tsirlis\Dropbox\My Desktop\Mourao - Miranda\Atlases_Mikael\warp_atlas')
basedir = 'C:\Users\Konstantinos Tsirlis\Dropbox\My Desktop\Mourao - Miranda\Atlases_Mikael\warp_atlas\';

% parameters
p_mb_mu = [basedir 'mu_T1.nii'];  % MB atlas
p_atlas = [basedir 'Buckner2011_Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii'];  % your atlas
p_atlas_mri = [basedir 'colin27_t1_tal_lin.nii'];  % the colin T1w atlas is defined in the same space as the AAL atlas
% p_atlas_mri = [basedir 'single_subj_T1.nii'];
onam = 'BC17_c27';
odir = [basedir 'result'];


%% We fit MB to the atlas space T1w image
matlabbatch = {};
matlabbatch{1}.spm.tools.mb.run.mu.exist = {p_mb_mu};
matlabbatch{1}.spm.tools.mb.run.aff = 'Aff(3)';
matlabbatch{1}.spm.tools.mb.run.v_settings = [0.001 0 2 0.5 1];
matlabbatch{1}.spm.tools.mb.run.onam = onam;
matlabbatch{1}.spm.tools.mb.run.odir = {odir};
matlabbatch{1}.spm.tools.mb.run.cat = {{}};
matlabbatch{1}.spm.tools.mb.run.gmm.chan.images = {p_atlas_mri};
matlabbatch{1}.spm.tools.mb.run.gmm.chan.inu.inu_reg = 10000;
matlabbatch{1}.spm.tools.mb.run.gmm.chan.inu.inu_co = 40;
matlabbatch{1}.spm.tools.mb.run.gmm.chan.modality = 1;
matlabbatch{1}.spm.tools.mb.run.gmm.labels.false = [];
matlabbatch{1}.spm.tools.mb.run.gmm.pr.file = {};
matlabbatch{1}.spm.tools.mb.run.gmm.pr.hyperpriors = [];
matlabbatch{1}.spm.tools.mb.run.gmm.tol_gmm = 0.0005;
matlabbatch{1}.spm.tools.mb.run.gmm.nit_gmm_miss = 32;
matlabbatch{1}.spm.tools.mb.run.gmm.nit_gmm = 8;
matlabbatch{1}.spm.tools.mb.run.gmm.nit_appear = 4;
matlabbatch{1}.spm.tools.mb.run.accel = 0.8;
matlabbatch{1}.spm.tools.mb.run.min_dim = 8;
matlabbatch{1}.spm.tools.mb.run.tol = 0.001;
matlabbatch{1}.spm.tools.mb.run.sampdens = 2;
matlabbatch{1}.spm.tools.mb.run.save = true;
matlabbatch{1}.spm.tools.mb.run.nworker = 0;
spm_jobman('run', matlabbatch);


%% We warp the atlas to MB space using the deformation computed above
matlabbatch = {};
matlabbatch{1}.spm.util.defs.comp{1}.inv.comp{1}.def = {[basedir 'result\y_1_00001_colin27_t1_tal_lin_' onam '.nii']};
% matlabbatch{1}.spm.util.defs.comp{1}.inv.comp{1}.def = {[basedir 'result\y_1_00001_single_subj_T1_' onam '.nii']};
matlabbatch{1}.spm.util.defs.comp{1}.inv.space = {p_mb_mu};
matlabbatch{1}.spm.util.defs.out{1}.pull.fnames = {p_atlas};
matlabbatch{1}.spm.util.defs.out{1}.pull.savedir.saveusr = {[basedir 'result']};
matlabbatch{1}.spm.util.defs.out{1}.pull.interp = -1;
matlabbatch{1}.spm.util.defs.out{1}.pull.mask = 1;
matlabbatch{1}.spm.util.defs.out{1}.pull.fwhm = [0 0 0];
matlabbatch{1}.spm.util.defs.out{1}.pull.prefix = 'BC17_c27_';
spm_jobman('run', matlabbatch);