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Slepi/Code/Utilities/spm12/spm_read_vols.m
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spm_read_vols.m
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function [Y,XYZ] = spm_read_vols(V,mask)
% Read in entire image volumes
% FORMAT [Y,XYZ] = spm_read_vols(V,mask)
% V - vector of mapped image volumes to read in (from spm_vol)
% mask - implicit zero mask?
%
% Y - 4D matrix of image data, fourth dimension indexes images
% XYZ - 3xn matrix of XYZ locations returned (in mm)
%__________________________________________________________________________
%
% For image data types without a representation of NaN (see spm_type),
% implicit zero masking can be used. If mask is set, then zeros are
% treated as masked, and returned as NaN.
%__________________________________________________________________________
% Copyright (C) 1999-2013 Wellcome Trust Centre for Neuroimaging
% Andrew Holmes
% $Id: spm_read_vols.m 5731 2013-11-04 18:11:44Z guillaume $
%-Argument checks
%--------------------------------------------------------------------------
if nargin<2, mask = 0; end
if nargin<1, error('insufficient arguments'), end
spm_check_orientations(V);
%-Read in image data
%--------------------------------------------------------------------------
n = numel(V); %-#images
Y = zeros([V(1).dim(1:3),n]); %-image data matrix
for i=1:n, for p=1:V(1).dim(3)
Y(:,:,p,i) = spm_slice_vol(V(i),spm_matrix([0 0 p]),V(i).dim(1:2),0);
end, end
%-Apply implicit zero mask for image datatypes without a NaNrep
%--------------------------------------------------------------------------
if mask
%-Work out images without NaNrep
im = false(n,1);
for i=1:n, im(i)=~spm_type(V(i).dt(1),'NaNrep'); end
%-Mask
Y(Y(:,:,:,im)==0) = NaN;
end
%-Return as 3D matrix if single image
%--------------------------------------------------------------------------
if n==1, Y=Y(:,:,:,1); end
%-Compute XYZ co-ordinates (if required)
%--------------------------------------------------------------------------
if nargout>1
[R,C,P] = ndgrid(1:V(1).dim(1),1:V(1).dim(2),1:V(1).dim(3));
RCP = [R(:)';C(:)';P(:)'];
clear R C P
RCP(4,:) = 1;
XYZ = V(1).mat(1:3,:)*RCP;
end
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