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makeVasoAnatInterp.m
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makeVasoAnatInterp.m
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% makeVasoAnat.m
%
% usage: makeVasoAnatInterp()
% by: eli merriam
% date: 10/25/18
% purpose:
%
function retval = makeVasoAnatInterp()
% check arguments
if ~any(nargin == [0])
help makeVasoAnat
return
end
% create a new view and get some info
v = newView;
nScans = viewGet(v, 'nScans', 'BoldMC');
hdr = viewGet(v, 'niftihdr', 1);
scaleFactor = 3;
for iScan = 1 %:nScans
% load the bold scans
v = viewSet(v, 'curGroup', 'BoldMC');
M = viewGet(v, 'transforms');
v = viewSet(v, 'curGroup', 'Bold');
tSeriesBold = loadTSeries(v, iScan);
dims = size(tSeriesBold);
interpBold = zeros(dims(1)*scaleFactor, dims(2)*scaleFactor, dims(3)*scaleFactor, length(M));
disppercent(-inf, 'Interpolating BOLD scans');
for iFrame=1:length(M)
thisM = M{iFrame};
thisM = thisM*diag([1./[scaleFactor scaleFactor scaleFactor] 1]);
%interpBold(:,:,:,iFrame) = warpAffine3(tSeriesBold(:,:,:,iFrame), thisM, NaN, 0, 'cubic', dims(1:3)*scaleFactor);
interpBold(:,:,:,iFrame) = interpVolume(tSeriesBold(:,:,:,iFrame), thisM, dims(1:3)*scaleFactor);
disppercent(iFrame/length(M));
end
disppercent(inf);
% load the nulled scans
v = viewSet(v, 'curGroup', 'NulledMC');
M = viewGet(v, 'transforms');
v = viewSet(v, 'curGroup', 'Nulled');
tSeriesNulled = loadTSeries(v, iScan);
dims = size(tSeriesNulled);
interpNulled = zeros(dims(1)*scaleFactor, dims(2)*scaleFactor, dims(3)*scaleFactor, length(M));
disppercent(-inf, 'Interpolating Nulled scans');
for iFrame=1:length(M)
thisM = M{iFrame};
thisM = thisM*diag([1./[scaleFactor scaleFactor scaleFactor] 1]);
%interpNulled(:,:,:,iFrame) = warpAffine3(tSeriesNulled(:,:,:,iFrame), thisM, NaN, 0, 'cubic', dims(1:3)*scaleFactor);
interpNulled(:,:,:,iFrame) = interpVolume(tSeriesNulled(:,:,:,iFrame), thisM, dims(1:3)*scaleFactor);
disppercent(iFrame/length(M));
end
disppercent(inf);
% concat bold and nulled tSeries together
tSeries = cat(4, interpBold, interpNulled);
% compute 1 / (std/abs(mean))
cvar(:,:,:,iScan) = 1 / (nanstd(tSeries,[],4) ./ abs(nanmean(tSeries,4)));
end
% average across runs
vasoAnat = nanmedian(cvar,4);
% trim bad values
vasoAnat(isinf(vasoAnat)) = 0;
vasoAnat(isnan(vasoAnat)) = 0;
vasoAnat(vasoAnat>20) = 0;
% set the qform/sform
hdr = cbiSetNiftiQform(hdr,hdr.qform44*diag([1./[scaleFactor scaleFactor scaleFactor] 1]));
hdr = cbiSetNiftiSform(hdr,hdr.sform44*diag([1./[scaleFactor scaleFactor scaleFactor] 1]));
hdr.dim(2:4) = [size(vasoAnat)];
% % upsample some more
% scaleFactor = 3;
% xform = diag([1./[scaleFactor scaleFactor scaleFactor 1]]);
% vasoAnat = warpAffine3(vasoAnat, xform, NaN, 0, 'linear', size(vasoAnat)*scaleFactor);
% hdr = cbiSetNiftiQform(hdr,hdr.qform44*diag([1./[scaleFactor scaleFactor scaleFactor] 1]));
% hdr = cbiSetNiftiSform(hdr,hdr.sform44*diag([1./[scaleFactor scaleFactor scaleFactor] 1]));
% hdr.dim(2:4) = [size(vasoAnat)];
%
% % blur a bit to deal with interpolation error
% for iSlice = 1:size(vasoAnat,3);
% vasoAnat(:,:,iSlice) = blur(vasoAnat(:,:,iSlice));
% end
% set the file extension
niftiFileExtension = '.nii';
% Path
pathStr = fullfile(viewGet(view,'anatomydir'),['vasoAnatInterp',niftiFileExtension]);
% Write, though check for over-writing
saveFlag = 'Yes';
if exist([pathStr,'.mat'],'file')
if confirm
saveFlag = questdlg([pathStr,' already exists. Overwrite?'],...
'Save Overlay?','Yes','No','No');
end
end
if strcmp(saveFlag,'Yes')
fprintf('Saving %s...\n',pathStr);
[byteswritten,hdr] = cbiWriteNifti(pathStr, vasoAnat, hdr);
fprintf('done\n');
else
fprintf('Anatomy not saved...');
end
% Delete temporary views
deleteView(v);
return;