nii_reslice_target.m

function [outhdr, outimg] = nii_reslice_target(inhdr, inimg, tarhdr, linearInterp) 
%Reslice input image to match dimensions of target image (either to disk or memory)
%  inhdr: image to reslice- either filename of NIfTI header or loaded NIfTI header structure
%  inimg: (optional) NIfTI image data (only if inhdr is a structure)
%  tarhdr: image to match- either filename of NIfTI header or loaded NIfTI header structure
%  linearinterp: (optional) if false nearest neighbor interpolation, else trilinear interpolation (default)
% Outputs: if not specified, resliced image saved to disk, else returns resliced header and image
%Chris Rorden (2014) see John Ashburner and Ged Ridgway's reorient.m 
% http://opensource.org/licenses/BSD-2-Clause
%Examples
%  nii_reslice_target('T1_LM1001.nii','','jhu.nii',false);
% Next example shows how to use this without writing to disk
%  inhdr = spm_vol('T1_LM1001.nii'); %load header
%  inimg = spm_read_vols(inhdr); %load volume
%  tarhdr = spm_vol('jhu.nii'); %load header
%  [outhdr,outimg] = nii_reslice_target(inhdr,inimg, tarhdr); %resize in memory
%  spm_write_vol(outhdr,outimg); %save resized image
% Next example: specify target dimensions without explicitly providing a full header
%  tarhdr.mat = [-1 0 0 79; 0 1 0 -113; 0 0 1 -51; 0 0 0 1];
%  tarhdr.dim = [157 189 136];
%  nii_reslice_target('qCBV.nii','',tarhdr);

if ~exist('inhdr','var')
    inhdr = spm_select(1,'image','Select source image that will be resliced');
end
if ~exist('tarhdr','var')
    tarhdr = spm_select(1,'image','Select target image (source will be resliced to match target)');
end
if ~exist('linearInterp','var')
    linearInterp = true;
end
if ~isstruct(tarhdr)
    tarhdr = spm_vol(tarhdr); %load target header
    tarhdr = tarhdr(1); %in case target is multiple volume file
end
imgdim = tarhdr.dim(1:3);
if ~isstruct(inhdr)
    inhdr = spm_vol(inhdr); %load input header
    inhdr = inhdr(1); %if 4D, only process first volume
	inimg = spm_read_vols(inhdr); %load input image
end
if size(inimg,4) > 1
    inhdr = inhdr(1);
    inimg = inimg(:,:,:,1);
    fprintf('%s warning: only reslicing first volume of 4D image %s\n', mfilename, inhdr.fname);
end
outhdr            = inhdr;
[pth,nam,ext] = fileparts(outhdr.fname);
outhdr.fname      = fullfile(pth,['r' nam ext]);
outhdr.dim(1:3)   = imgdim(1:3);
outhdr.mat        = tarhdr.mat;
if isequal(inhdr.mat, outhdr.mat) && isequal(outhdr.dim(1:3), inhdr.dim(1:3))
    fprintf('%s no need to reslice: input image already aligned to target image\n', mfilename);
    outimg = inimg;
else %if reslicing is required
    outimg = zeros(outhdr.dim(1:3));
    for i = 1:imgdim(3)
        M = inv(spm_matrix([0 0 -i])*inv(outhdr.mat)*inhdr.mat);
        if linearInterp
            outimg(:,:,i) = spm_slice_vol(inimg, M, imgdim(1:2), 1); % (linear interp)
        else
            outimg(:,:,i) = spm_slice_vol(inimg, M, imgdim(1:2), 0); % (nearest neighbor interp)
        end
    end
end
if nargout < 2
    outhdr = spm_create_vol(outhdr); %save header to disk
    spm_write_vol(outhdr,outimg); %save image to disk
end
%end nii_reslice_target()