/
ROI_registration_spm.m
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ROI_registration_spm.m
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function ROI_registration_spm(WD,ROI,SUB_LIST,POOLSIZE,TEMPLATE,LEFT,RIGHT)
%-----------------------------------------------------------------------
% transform ROIs from MNI space to DTI(b0) space
%-----------------------------------------------------------------------
SUB = textread(SUB_LIST,'%s');
% make ROIs be proper datatype, default double
if LEFT == 1
ROI_L=[WD,'/ROI/',ROI,'_L.nii'];
roi_l=load_untouch_nii(ROI_L);
roi_l.hdr.dime.datatype=64;
roi_l.hdr.dime.bitpix=64;
roi_l.img=double(roi_l.img);
save_untouch_nii(roi_l,ROI_L);
end
if RIGHT == 1
ROI_R=[WD,'/ROI/',ROI,'_R.nii'];
roi_r=load_untouch_nii(ROI_R);
roi_r.hdr.dime.datatype=64;
roi_r.hdr.dime.bitpix=64;
roi_r.img=double(roi_r.img);
save_untouch_nii(roi_r,ROI_R);
end
% 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
% coregister T1 to b0 space
parfor i=1:length(SUB)
spm_coreg_ew(WD,SUB,i)
end
matlabbatch=[];
% coregistered T1 image from b0 to MNI space
parfor i=1:length(SUB)
spm_norm_e(WD,SUB,i,TEMPLATE)
end
matlabbatch=[];
% ROIs from MNI space to b0 space using inverse matrix
if LEFT == 1
parfor i=1:length(SUB)
spm_util_deform(WD,SUB,i,ROI_L)
end
matlabbatch=[];
end
if RIGHT == 1
parfor i=1:length(SUB)
spm_util_deform(WD,SUB,i,ROI_R)
end
matlabbatch=[];
end
% close pool
if exist('parpool')
delete(p);
else
matlabpool close;
end
function spm_coreg_ew(WD,SUB,i)
sourcepath = strcat(WD,'/',SUB{i});
disp(sourcepath);
b0refimg = strcat(sourcepath,'/b0_',SUB{i},'.nii');
T1sourceimg = strcat(sourcepath,'/T1_',SUB{i},'.nii');
spm('defaults','fmri');
spm_jobman('initcfg');
matlabbatch{1}.spm.spatial.coreg.estwrite.ref = {b0refimg};
matlabbatch{1}.spm.spatial.coreg.estwrite.source = {T1sourceimg};
matlabbatch{1}.spm.spatial.coreg.estwrite.other = {''};
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.cost_fun = 'nmi';
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.sep = [4 2];
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.tol = [0.002 0.002 0.002 0.0001 0.0001 0.0001 0.001 0.001 0.001 0.0001 0.0001 0.0001];
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.fwhm = [7 7];
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.interp = 1;
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.wrap = [0 0 0];
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.mask = 0;
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.prefix = 'r';
spm_jobman('run',matlabbatch)
function spm_norm_e(WD,SUB,i,TEMPLATE)
sourcepath = strcat(WD,'/',SUB{i});
disp(sourcepath);
sourceimg = strcat(sourcepath,'/rT1_',SUB{i},'.nii');
spm('defaults','fmri');
spm_jobman('initcfg');
matlabbatch{1}.spm.spatial.normalise.est.subj.source = {sourceimg};
matlabbatch{1}.spm.spatial.normalise.est.subj.wtsrc = '';
matlabbatch{1}.spm.spatial.normalise.est.eoptions.template = {TEMPLATE};
matlabbatch{1}.spm.spatial.normalise.est.eoptions.weight = '';
matlabbatch{1}.spm.spatial.normalise.est.eoptions.smosrc = 8;
matlabbatch{1}.spm.spatial.normalise.est.eoptions.smoref = 0;
matlabbatch{1}.spm.spatial.normalise.est.eoptions.regtype = 'mni';
matlabbatch{1}.spm.spatial.normalise.est.eoptions.cutoff = 25;
matlabbatch{1}.spm.spatial.normalise.est.eoptions.nits = 16;
matlabbatch{1}.spm.spatial.normalise.est.eoptions.reg = 1;
spm_jobman('run',matlabbatch)
function spm_util_deform(WD,SUB,i,ROI)
sourcepath = strcat(WD,'/',SUB{i});
disp(sourcepath);
roimat = strcat(sourcepath,'/rT1_',SUB{i},'_sn.mat');
refimg = strcat(sourcepath,'/rT1_',SUB{i},'.nii');
spm('defaults','fmri');
spm_jobman('initcfg');
matlabbatch{1}.spm.util.defs.comp{1}.inv.comp{1}.sn2def.matname = {roimat};
matlabbatch{1}.spm.util.defs.comp{1}.inv.space = {refimg};
matlabbatch{1}.spm.util.defs.comp{1}.inv.comp{1}.sn2def.vox = [NaN NaN NaN];
matlabbatch{1}.spm.util.defs.comp{1}.inv.comp{1}.sn2def.bb = [NaN NaN NaN
NaN NaN NaN];
matlabbatch{1}.spm.util.defs.ofname = '';
matlabbatch{1}.spm.util.defs.fnames = {ROI};
matlabbatch{1}.spm.util.defs.savedir.saveusr = {sourcepath};
matlabbatch{1}.spm.util.defs.interp = 0;
spm_jobman('run',matlabbatch)