ROI_toMNI_spm_xmm.m

function ROI_toMNI_spm_xmm(WD,ROI,SUB_LIST,MAX_CL_NUM,POOLSIZE,TEMPLATE,VOX_SIZE,METHOD,LEFT,RIGHT)
%-----------------------------------------------------------------------
% transform ROIs from DTI(b0) space to MNI space
%-----------------------------------------------------------------------

SUB = textread(SUB_LIST,'%s');

% Parallel Computing Toolbox settings
% 2014a removed findResource, replaced by parcluster
% 2016b removed matlabpool, replaced by parpool

% modify temporary dir
temp_dir=tempname();
mkdir(temp_dir);
if exist('parcluster')
	pc=parcluster('local');
	pc.JobStorageLocation=temp_dir;
else
	sched=findResource('scheduler','type','local');
	sched.DataLocation=temp_dir;
end

% open pool
if exist('parpool')
	p=parpool('local',POOLSIZE);
else
	matlabpool('local',POOLSIZE);
end


if LEFT == 1
	parfor i=1:length(SUB)
		spm_norm_ew(WD,SUB,i,ROI,MAX_CL_NUM,METHOD,TEMPLATE,VOX_SIZE,'L')
	end
	matlabbatch=[];
end

if RIGHT == 1
	parfor i=1:length(SUB)
		spm_norm_ew(WD,SUB,i,ROI,MAX_CL_NUM,METHOD,TEMPLATE,VOX_SIZE,'R')
	end
	matlabbatch=[];
end

% close pool
if exist('parpool')
	delete(p);
else
	matlabpool close;
end


function spm_norm_ew(WD,SUB,i,ROI,MAX_CL_NUM,METHOD,TEMPLATE,VOX_SIZE,LR)
	sourcepath=strcat(WD,'/',SUB{i});
	disp(sourcepath);
	sourceimg=strcat(sourcepath,'/rT1_',SUB{i},'.nii');
	for N=2:MAX_CL_NUM
		resampleimg{N}=strcat(sourcepath,'/',SUB{i},'_',ROI,'_',LR,'_',METHOD,'/',ROI,'_',LR,'_',num2str(N),'.nii');
	end

	spm('defaults','fmri');
	spm_jobman('initcfg');

	for N = 2:MAX_CL_NUM
		matlabbatch{1}.spm.spatial.normalise.estwrite.subj.source = {sourceimg};
		matlabbatch{1}.spm.spatial.normalise.estwrite.subj.wtsrc = '';
		matlabbatch{1}.spm.spatial.normalise.estwrite.subj.resample = {resampleimg{N}};
 		matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.template = {TEMPLATE};
 		matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.weight = {''};
 		matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.smosrc = 8;
 		matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.smoref = 0;
 		matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.regtype = 'mni';
 		matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.cutoff = 25;
 		matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.nits = 16;
 		matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.reg = 1;
 		matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.preserve = 0;
 		matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.bb = [-90 -126 -72
                                                              		  90 90 108];
 		matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.vox = [VOX_SIZE VOX_SIZE VOX_SIZE];
 		matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.interp = 0;
 		matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.wrap = [0 0 0];
 		matlabbatch{1}.spm.spatial.normalise.estwrite.roptions.prefix = 'w';

 		spm_jobman('run',matlabbatch)
	end
	
	disp(strcat(SUB{i},'_',LR,' Done!'));