Intersubj_pipeline/JOVE_AtlasData.m
43995c3ce32fmaster

JOVE_AtlasData.m
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			function [TC] = JOVE_AtlasData(Data,GM,Atlas,iy,FF)

			% Converts the atlas into native space at the proper resolution (nearest
			% neighbour interpolation
			spm_jobman('initcfg')

			matlabbatch{1}.spm.spatial.normalise.write.subj.def = {iy};
			matlabbatch{1}.spm.spatial.normalise.write.subj.resample = {Atlas};
			% matlabbatch{1}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70
			% 78 76 85];

			matlabbatch{1}.spm.spatial.normalise.write.woptions.bb = [-85 -112 -85
			85 120 85];
			matlabbatch{1}.spm.spatial.normalise.write.woptions.vox = [2 2 2];
			matlabbatch{1}.spm.spatial.normalise.write.woptions.interp = 0;

			% This will save the normalized version
			spm_jobman('run',matlabbatch);

			tmp_string = strsplit(Atlas,'/');

			tmp_atlas = '/';

			for i = 2:length(tmp_string)
			if i < length(tmp_string)
			tmp_atlas = [tmp_atlas,tmp_string{i},'/'];
			else
			tmp_atlas = [tmp_atlas,'w',tmp_string{i}];
			end
			end

			ATLAS = mapVolumeToVolume(tmp_atlas,FF);
			ATLAS = ATLAS(:);

			ATLAS(isnan(ATLAS)) = 0;
			ATLAS(~GM) = 0;

			[TC] = Make_Atlasing(Data,ATLAS);

			clear ATLAS

			end