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spm_ROI.m
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spm_ROI.m
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function [xY, XYZmm, j] = spm_ROI(xY, XYZmm)
% Region of Interest specification
% FORMAT xY = spm_ROI(xY)
% xY - VOI structure
% xY.def - VOI definition [sphere, box, mask, cluster, all]
% xY.rej - cell array of disabled VOI definition options
% xY.xyz - centre of VOI {mm}
% xY.spec - VOI definition parameters
% xY.str - description of the VOI
%
% FORMAT [xY, XYZmm, j] = spm_ROI(xY, XYZmm)
% XYZmm - [3xm] locations of voxels {mm}
% If an image filename, an spm_vol structure or a NIfTI object is
% given instead, XYZmm will be initialised to all voxels within
% the field of view of that image.
%
% XYZmm - [3xn] filtered locations of voxels {mm} (m>=n) within VOI xY
% j - [1xn] indices of input locations XYZmm within VOI xY
%__________________________________________________________________________
% Copyright (C) 2008-2014 Wellcome Trust Centre for Neuroimaging
% Karl Friston, Guillaume Flandin
% $Id: spm_ROI.m 6079 2014-06-30 18:25:37Z spm $
if nargin < 2 && nargout > 1
error('Too many output arguments.');
end
try, xY; catch, xY = []; end
%-Specify ROI
%==========================================================================
if ~isfield(xY,'def')
def = {'sphere','box','cluster','mask'};
if isfield(xY,'rej')
if ~isfield(xY,'M')
xY.rej = {xY.rej{:} 'cluster'};
end
else
if isfield(xY,'M')
xY.rej = {};
else
xY.rej = {'cluster'};
end
end
[q, i] = setdiff(def,xY.rej);
def = def(sort(i));
xY.def = spm_input('VOI definition...','!+1','b',def,[],1);
end
%-ROI parameters
%--------------------------------------------------------------------------
switch lower(xY.def)
case 'sphere'
%----------------------------------------------------------------------
if ~isfield(xY,'xyz') || isempty(xY.xyz)
xY.xyz = spm_input('sphere centre [x y z] {mm}',...
'!+0','r','0 0 0',3);
end
if ~isfield(xY,'spec')
xY.spec = spm_input('sphere radius (mm)','!+0','r',0,1,[0,Inf]);
end
xY.str = sprintf('%0.1fmm sphere',xY.spec);
case 'box'
%----------------------------------------------------------------------
if ~isfield(xY,'xyz') || isempty(xY.xyz)
xY.xyz = spm_input('box centre [x y z] {mm}',...
'!+0','r','0 0 0',3);
end
if ~isfield(xY,'spec')
xY.spec = spm_input('box dimensions [x y z] {mm}',...
'!+0','r','0 0 0',3);
end
if length(xY.spec) < 3
xY.spec = xY.spec(1)*[1 1 1];
end
xY.str = sprintf('%0.1f x %0.1f x %0.1f mm box',xY.spec);
case 'mask'
%----------------------------------------------------------------------
if ~isfield(xY,'spec')
xY.spec = spm_vol(spm_select(1,'image','Specify Mask'));
else
if ~isstruct(xY.spec)
xY.spec = spm_vol(xY.spec);
end
end
str = spm_file(xY.spec.fname,'short30');
str = regexprep(str, {'\\' '\^' '_' '{' '}'}, ...
{'\\\\' '\\^' '\\_' '\\{' '\\}'}); % Escape TeX special characters
xY.str = sprintf('image mask: %s',str);
case 'cluster'
%----------------------------------------------------------------------
if ~isfield(xY,'xyz') || isempty(xY.xyz)
xY.xyz = spm_input('seed voxel [x y z] {mm}',...
'!+0','r','0 0 0',3);
end
if ~isfield(xY,'M')
xY.M = spm_input('affine transformation matrix',...
'!+0','r','0 0 0',[4 4]);
end
xY.spec = [];
xY.str = sprintf('cluster (seed voxel: %0.1f %0.1f %0.1f)',xY.xyz);
case 'all'
%----------------------------------------------------------------------
xY.str = 'all';
otherwise
%----------------------------------------------------------------------
error('Unknown VOI type.');
end
if nargin < 2, return; end
%-'Estimate' ROI
%==========================================================================
%-Argument check
%--------------------------------------------------------------------------
if ischar(XYZmm) && isempty(XYZmm)
XYZmm = spm_select(1,'image','Specify Image');
end
if ischar(XYZmm), XYZmm = spm_vol(XYZmm); end
if isa(XYZmm,'nifti')
XYZmm = struct('dim',size(XYZmm.dat), 'mat',XYZmm.mat);
end
if isstruct(XYZmm) % spm_vol
[R,C,P] = ndgrid(1:XYZmm.dim(1),1:XYZmm.dim(2),1:XYZmm.dim(3));
RCP = [R(:)';C(:)';P(:)';ones(1,numel(R))];
XYZmm = XYZmm.mat(1:3,:)*RCP;
clear R C P RCP
end
if isempty(XYZmm), XYZmm = zeros(3,0); end
%-Filter location of voxels
%--------------------------------------------------------------------------
Q = ones(1,size(XYZmm,2));
switch lower(xY.def)
case 'sphere'
%----------------------------------------------------------------------
j = find(sum((XYZmm - xY.xyz*Q).^2) <= xY.spec^2);
case 'box'
%----------------------------------------------------------------------
j = find(all(abs(XYZmm - xY.xyz*Q) <= xY.spec(:)*Q/2));
case 'mask'
%----------------------------------------------------------------------
XYZ = xY.spec.mat \ [XYZmm; Q];
j = find(spm_sample_vol(xY.spec, XYZ(1,:), XYZ(2,:), XYZ(3,:),0) > 0);
case 'cluster'
%----------------------------------------------------------------------
[x, i] = spm_XYZreg('NearestXYZ',xY.xyz,XYZmm);
XYZ = round(xY.M \ [XYZmm; Q]);
A = spm_clusters(XYZ);
j = find(A == A(i));
case 'all'
%----------------------------------------------------------------------
j = 1:size(XYZmm,2);
otherwise
%----------------------------------------------------------------------
error('Unknown VOI type.');
end
XYZmm = XYZmm(:,j);
if strcmpi(xY.def,'mask') && ~isempty(XYZmm), xY.xyz = mean(XYZmm,2); end