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wIMM_creation.m
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function wIMM_creation(antspath, afnipath, fmriprepdir, templatepath, thresholds, numcomps, templateMNIspace)
inputsubs=dir(fmriprepdir);
subs = {inputsubs.name};
subs = subs(3:length(subs));
thresholds = [thresholds 1.96];
for subi = 1:length(subs)
disp(char(subs(subi)))
subid = char(subs(subi));
tic;
if ~isfolder([fmriprepdir subid '/template/'])
mkdir([fmriprepdir subid '/template/'])
end
inputfilename = dir([[fmriprepdir char(subs(subi)) '/func/'], '*_task-rest*_space-T1w_desc-preproc_bold.nii.gz']);
if ~isempty(inputfilename)
nativetemplatepath = [fmriprepdir char(subs(subi)) '/template/template_native.nii'];
nativize_template_str = [antspath ' -i ' templatepath ' -t ' fmriprepdir char(subs(subi)) '/anat/' char(subs(subi)) '_from-' templateMNIspace '_to-T1w_mode-image_xfm.h5 ' ' -r ' fmriprepdir char(subs(subi)) '/anat/' char(subs(subi)) '_desc-preproc_T1w.nii.gz -o ' nativetemplatepath];
if ~exist(nativetemplatepath, 'file')
system(nativize_template_str);
end
templatedeob = [fmriprepdir char(subs(subi)) '/template/template_native_deoblique.nii'];
templateresample = [fmriprepdir char(subs(subi)) '/template/template_native_resample.nii'];
if ~isfile(templatedeob)
system([afnipath '/3dWarp -deoblique -overwrite -prefix ' templatedeob ' ' nativetemplatepath]);
end
if ~isfile(templateresample)
system([afnipath '/3dresample -overwrite -master ' fmriprepdir char(subs(subi)) '/restmelodicsmooth_auto/mean.nii.gz -prefix ' templateresample ' -input ' templatedeob]);
end
template = spm_read_vols(spm_vol(templateresample));
template = template>0;
topdicis = zeros(length(numcomps),length(thresholds));
topdici_ind = 1;
topdici_thresh = zeros(length(numcomps),length(thresholds));
for numi = numcomps
outdir = [fmriprepdir char(subs(subi)) '/restmelodicsmooth_' char(numi)];
if ~isfile([outdir '/melodic_IC.nii'])
gunzip([outdir '/melodic_IC.nii.gz']);
end
nummelodic=spm_read_vols(spm_vol([outdir '/melodic_IC.nii']));
brainmaskfile = [outdir '/mask.nii'];
if ~isfile (brainmaskfile)
gunzip([brainmaskfile '.gz']);
end
brainmask = spm_read_vols(spm_vol(brainmaskfile));
dici_template=zeros(size(nummelodic,4),1);
hr_template=zeros(size(nummelodic,4),1);
far_template=zeros(size(nummelodic,4),1);
noise_template = zeros(size(nummelodic,4),1);
hr_far_diff_template = zeros(size(nummelodic,4),1);
for compi = 1:size(nummelodic,4)
zind = 1;
for zi = thresholds
component=squeeze(nummelodic(:,:,:,compi));
component = component>zi;
intersect_template = component & template;
hitrate_template = sum(intersect_template(:))/sum(template(:));
if hitrate_template==1
hitrate_template = (sum(template(:))-1)/sum(template(:));
elseif hitrate_template==0
hitrate_template = 1/sum(template(:));
end
falsealarm_template = component & ~template & brainmask;
outsidetemplate_insidebrainmask = ~template & brainmask;
falsealarmrate_template = (sum(falsealarm_template(:))/sum(outsidetemplate_insidebrainmask(:)));
if falsealarmrate_template==1
falsealarmrate_template = (sum(outsidetemplate_insidebrainmask(:))-1)/sum(outsidetemplate_insidebrainmask(:));
elseif falsealarmrate_template==0
falsealarmrate_template = 1/sum(outsidetemplate_insidebrainmask(:));
end
hr_far_template = norminv(hitrate_template, 0, 1)-norminv(falsealarmrate_template, 0, 1);
dici_template(compi, zind) = hr_far_template;
hr_template(compi, zind) = hitrate_template;
far_template(compi, zind) = falsealarmrate_template;
noise_template(compi, zind) = sum(falsealarm_template(:))/sum(component(:));
hr_far_diff_template(compi, zind) = (hitrate_template - falsealarmrate_template);
zind = zind+1;
end
end
[~,i] = sort(dici_template, 'descend');
[comp, ~,vals] = mode(i(:,1:length(thresholds)-1),2);
if(length(vals(1))>1)
maxdici = -Inf;
maxcomp = 0;
for vali = 1:length(vals{1})
valcomp = vals{1}(vali);
dici196 = dici_template(valcomp, length(thresholds));
if dici196>maxdici
maxdici = dici196;
maxcomp = valcomp;
end
end
topdicis(topdici_ind, 1) = maxcomp;
topdicis(topdici_ind, 2) = maxdici;
topdicis(topdici_ind, 3) = hr_template(maxcomp, length(thresholds));
topdicis(topdici_ind, 4) = far_template(maxcomp, length(thresholds));
topdicis(topdici_ind, 5) = noise_template(maxcomp, length(thresholds));
topdicis(topdici_ind, 6) = hr_far_diff_template(maxcomp, length(thresholds));
else
topdicis(topdici_ind, 1) = comp(1);
topdicis(topdici_ind, 2) = dici_template(comp(1), length(thresholds));
topdicis(topdici_ind, 3) = hr_template(comp(1), length(thresholds));
topdicis(topdici_ind, 4) = far_template(comp(1), length(thresholds));
topdicis(topdici_ind, 5) = noise_template(comp(1), length(thresholds));
topdicis(topdici_ind, 6) = hr_far_diff_template(comp(1), length(thresholds));
end
topdici_thresh(topdici_ind, :) = dici_template(topdicis(topdici_ind, 1), :);
topdici_ind = topdici_ind+1;
end
ncoltopdicis = size(topdicis,2);
for topi = 1:size(topdicis,1)
tncmelodic = spm_read_vols(spm_vol([fmriprepdir subid '/restmelodicsmooth_' char(numcomps(topi)) '/melodic_IC.nii']));
tnctopcomp = squeeze(tncmelodic(:,:,:,topdicis(topi,1)));
[~, idx] = max(tnctopcomp(:));
[r,c,p] = ind2sub(size(tnctopcomp), idx);
if topi ==1
topdicis(topi,ncoltopdicis+1) = 0;
else
topdicis(topi,ncoltopdicis+1) = str2double(char(numcomps(topi)));
end
topdicis(topi,ncoltopdicis+2) = 0;
for ri = max(r-1,1):min(r+1,size(tncmelodic,1))
for ci = max(c-1,1):min(c+1,size(tncmelodic,2))
for pi = max(p-1,1):min(p+1,size(tncmelodic,3))
if template(ri,ci,pi)==1
topdicis(topi,ncoltopdicis+2) = 1;
end
end
end
end
end
topdicis = topdicis(topdicis(:,ncoltopdicis+2)==1,:);
[~,I] = max(topdicis(:,2));
if topdicis(I,ncoltopdicis+1)==0
outdir = [fmriprepdir subid '/restmelodicsmooth_auto'];
else
outdir = [fmriprepdir subid '/restmelodicsmooth_' num2str(topdicis(I,ncoltopdicis+1))];
end
nummelodic = spm_read_vols(spm_vol([outdir '/melodic_IC.nii']));
dici_templatefinal=zeros(size(nummelodic,4),1);
for compi = 1:size(nummelodic,4)
zind = 1;
for zi = thresholds(1:length(thresholds)-1)
component=squeeze(nummelodic(:,:,:,compi));
component = component>zi;
intersect_templatefinal = component & template;
hitrate_templatefinal = sum(intersect_templatefinal(:))/sum(template(:));
if hitrate_templatefinal==1
hitrate_templatefinal = (sum(template(:))-1)/sum(template(:));
elseif hitrate_templatefinal==0
hitrate_templatefinal = 1/sum(template(:));
end
falsealarm_templatefinal = component & ~template & brainmask;
outsidetemplate_insidebrainmask = ~template & brainmask;
falsealarmrate_templatefinal = (sum(falsealarm_templatefinal(:))/sum(outsidetemplate_insidebrainmask(:)));
if falsealarmrate_templatefinal==1
falsealarmrate_templatefinal = (sum(outsidetemplate_insidebrainmask(:))-1)/sum(outsidetemplate_insidebrainmask(:));
elseif falsealarmrate_templatefinal==0
falsealarmrate_templatefinal = 1/sum(outsidetemplate_insidebrainmask(:));
end
hr_far_templatefinal = norminv(hitrate_templatefinal, 0, 1)-norminv(falsealarmrate_templatefinal, 0, 1);
dici_templatefinal(compi, zind) = hr_far_templatefinal;
zind = zind+1;
end
end
meandici = transpose(mean(dici_templatefinal,2));
[~, maxmeandiciind] = max(meandici);
[sortvals, ~] = sort(meandici,'descend');
sortmeandiffs = abs(diff(sortvals));
maxdiff = max(sortmeandiffs);
[~, data2cluster, cluster2dataCell] = MeanShiftCluster(meandici,maxdiff);
maxclust = cell2mat(cluster2dataCell(data2cluster(maxmeandiciind)));
finalnumcomps = 0;
finalnetwork = zeros(size(brainmask));
for clustcompi = 1:length(maxclust)
onevoxpeakcheck = 0;
clustcomp = squeeze(nummelodic(:,:,:,maxclust(clustcompi)));
[~, idx] = max(clustcomp(:));
[r,c,p] = ind2sub(size(clustcomp), idx);
for ri = max(r-1,1):min(r+1,size(tncmelodic,1))
for ci = max(c-1,1):min(c+1,size(tncmelodic,2))
for pi = max(p-1,1):min(p+1,size(tncmelodic,3))
if template(ri,ci,pi)==1
onevoxpeakcheck = 1;
end
end
end
end
if onevoxpeakcheck==1
compheader = spm_vol([outdir '/mean.nii']);
outdirsplit = split(outdir, '_');
compheader.fname = [fmriprepdir subid '/' subid '_TNC_' char(outdirsplit(2)) '_component_' num2str(maxclust(clustcompi)) '.nii'];
compheader.private.dat.fname = compheader.fname;
spm_write_vol(compheader, clustcomp);
finalnumcomps = finalnumcomps+1;
overlapclust = finalnetwork & clustcomp;
if sum(overlapclust(:)) == 0
finalnetwork = finalnetwork+clustcomp;
else
finalnetworkoverlap = finalnetwork;
finalnetworkoverlap(~overlapclust) = 0;
clustcompoverlap = clustcomp;
clustcompoverlap(~overlapclust) = 0;
clustcomp(overlapclust) = 0;
finalnetwork(overlapclust) = 0;
overlapclust = double(overlapclust);
for i = 1:size(overlapclust,1)
for j = 1:size(overlapclust,2)
for k = 1:size(overlapclust,3)
if overlapclust(i,j,k)==1
overlapclust(i,j,k) = max(finalnetworkoverlap(i,j,k), clustcompoverlap(i,j,k));
end
end
end
end
finalnetwork = finalnetwork+clustcomp;
finalnetwork = finalnetwork+overlapclust;
end
end
end
if ~isfile([outdir '/mean.nii'])
gunzip([outdir '/mean.nii.gz' ]);
end
compheader = spm_vol([outdir '/mean.nii']);
compheader.fname = [fmriprepdir subid '/' subid '_final_ICA_map.nii'];
compheader.private.dat.fname = compheader.fname;
spm_write_vol(compheader, finalnetwork);
end
toc;
end
end