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function smooth_data_out = aedes_fmri_smooth(data,fwhm_sz,voxsize,out_file) | |
if nargin==4 | |
writeSmoothedData = true; | |
else | |
writeSmoothedData = false; | |
end | |
if nargin<3 || isempty(voxsize) | |
fwhmInPixels = true; | |
else | |
fwhmInPixels = false; | |
end | |
% Check if data is an Aedes structure | |
if isstruct(data) | |
data = data.FTDATA; | |
elseif ischar(data) | |
data = aedes_data_read(data); | |
data = data.FTDATA; | |
end | |
UseImFilter = true; | |
smooth_data = zeros(size(data)); | |
% Check data dimensions | |
if any(ndims(data)==[4,3]) && size(data,3)~=1 | |
use3Dkernel = true; | |
else | |
use3Dkernel = false; | |
end | |
% Calculate standard deviations using FWHM | |
if fwhmInPixels | |
stds = fwhm_sz/sqrt(8*log(2)); | |
else | |
stds = (fwhm_sz/sqrt(8*log(2)))./voxsize; | |
end | |
% Calculate kernel size using STDs | |
kernel_sz = round(6*stds); | |
if kernel_sz(3)>floor((size(data,3)/2)) | |
kernel_sz(3)=floor((size(data,3)-1)/2); | |
end | |
% Construct the smoothing kernel | |
if use3Dkernel | |
[x,y,z] = meshgrid(-kernel_sz(2):kernel_sz(2),... | |
-kernel_sz(1):kernel_sz(1),... | |
-kernel_sz(3):kernel_sz(3)); | |
s_kernel = exp(-(x).^2/(2*(stds(1)).^2)... | |
-(y).^2/(2*(stds(2)).^2)... | |
-(z).^2/(2*(stds(3)).^2)); | |
s_kernel = s_kernel/sum(s_kernel(:)); | |
else | |
[x,y] = meshgrid(-kernel_sz(2):kernel_sz(2),... | |
-kernel_sz(1):kernel_sz(1)); | |
s_kernel = exp(-(x).^2/(2*(stds(1)).^2)... | |
-(y).^2/(2*(stds(2)).^2)); | |
s_kernel = s_kernel/sum(s_kernel(:)); | |
end | |
% Smooth the image data ----------------------- | |
nVols = size(data,4); | |
if ~UseImFilter | |
tmp_sz = size(data(:,:,:,1)); | |
%tmp_sz(3)=tmp_sz(3)+fwhm_sz(3); | |
%ind_hi=ceil(tmp_sz/2)+floor(size(s_kernel)/2); | |
%ind_lo=ind_hi-(size(s_kernel)-1); | |
%ind_lo(ind_lo<1)=1; | |
%tmp_kernel = zeros(tmp_sz); | |
%tmp_kernel((ind_lo(1):ind_hi(1))+1,(ind_lo(2):ind_hi(2))+1,... | |
% (ind_lo(3):ind_hi(3)))=s_kernel; | |
tmp_kernel = s_kernel; | |
tmp_kernel(tmp_sz(1),tmp_sz(2),tmp_sz(3))=0; % Pad with zeros | |
end | |
for ii=1:nVols | |
if ii==1 | |
fprintf(1,'Smoothing volume %d/%d',ii,nVols); | |
bsz = length(sprintf('%d/%d',ii,nVols)); | |
else | |
fprintf(1,repmat('\b',1,bsz)); | |
bsz = length(sprintf('%d/%d',ii,nVols)); | |
fprintf(1,'%d/%d',ii,nVols); | |
end | |
if UseImFilter | |
tmp_data = data(:,:,:,ii); | |
smooth_data(:,:,:,ii) = imfilter(tmp_data,s_kernel); | |
else | |
tmp_data = double(data(:,:,:,ii)); | |
%pad_sz=size(tmp_data)+fwhm_sz*2; | |
%tmp_data(pad_sz(1),pad_sz(2),pad_sz(3))=0; | |
%tmp_data = cat(3,tmp_data(:,:,1),tmp_data,tmp_data(:,:,end)); | |
tmp_smooth = fftshift(ifftn(fftn(tmp_data).*fftn(tmp_kernel)),3); | |
smooth_data(:,:,:,ii) = tmp_smooth;%tmp_smooth(:,:,1:size(data,3)); | |
end | |
end | |
fprintf(1,'\n'); | |
if nargout>0 | |
smooth_data_out = smooth_data; | |
end | |
% Write output files | |
if writeSmoothedData | |
aedes_write_nifti(smooth_data,out_file) | |
end |