imtool3D_nii_crop.m

function imtool3D_nii_crop(filename)
% imtool3D_nii_crop     crop a nifti image
%   imtool3D_nii_crop(filename) opens a .nii(.gz) file in a imtool3D_3plane 
%   instance with rectangles in each plane. User can manipulate the  
%   rectangles. When set, user close the figure and a croped .nii file
%   is created with the suffix _crop.
%   It requires the dicm2nii package https://github.com/xiangruili/dicm2nii

if ~isdeployed
    if ~exist('filename','var'), help imtool3D_nii_crop; return; end
    if ~exist(filename,'file'), error(['can''t find nifti file ' filename]); end
    A = which('nii_tool');
    if isempty(A)
        error('Dependency to Xiangrui Li NIFTI tools is missing. http://www.mathworks.com/matlabcentral/fileexchange/42997');
    end
end

% open image in imtool3D
nii = nii_tool('load',filename);
tool = imtool3D_nii_3planes(nii);

% add synchronized rectangles
RECTS = imtool3D_3planes_rect(tool.getTool);

% wait for user to close figure
waitfor(tool.getHandles.fig);

% get Rectrangles positions and crop
pos = RECTS(1).getPosition();
cut_from_L = floor(pos(2)-pos(4)/2);
cut_from_R = floor(pos(2)+pos(4)/2);
cut_from_P = floor(pos(1)-pos(3)/2);
cut_from_A = floor(pos(1)+pos(3)/2);
pos = RECTS(2).getPosition();
cut_from_I = floor(pos(1)-pos(3)/2);
cut_from_S = floor(pos(1)+pos(3)/2);

nii.img = nii.img( max(1,cut_from_L+1) : min(end,cut_from_R), ...
			   max(1,cut_from_P+1) : min(end,cut_from_A), ...
			   max(1,cut_from_I+1) : min(end,cut_from_S), ...
			   :,:,:,:,:);
     

% adapt the quaternion
b = nii.hdr.quatern_b;
c = nii.hdr.quatern_c;
d = nii.hdr.quatern_d;

if 1.0-(b*b+c*c+d*d) < 0
   if abs(1.0-(b*b+c*c+d*d)) < 1e-5
       a = 0;
   else
       error('Incorrect quaternion values in this NIFTI data.');
   end
else
   a = sqrt(1.0-(b*b+c*c+d*d));
end

R = [a*a+b*b-c*c-d*d     2*b*c-2*a*d        2*b*d+2*a*c
   2*b*c+2*a*d         a*a+c*c-b*b-d*d    2*c*d-2*a*b
   2*b*d-2*a*c         2*c*d+2*a*b        a*a+d*d-c*c-b*b];

qmod = R*[cut_from_L*nii.hdr.pixdim(2);cut_from_P*nii.hdr.pixdim(3);cut_from_I*nii.hdr.pixdim(4)*nii.hdr.pixdim(1)];
nii.hdr.qoffset_x = nii.hdr.qoffset_x + qmod(1);
nii.hdr.qoffset_y = nii.hdr.qoffset_y + qmod(2);
nii.hdr.qoffset_z = nii.hdr.qoffset_z + qmod(3);

nii.hdr.srow_x(4) = nii.hdr.srow_x(4) + ...
                    nii.hdr.srow_x(1)*cut_from_L + ...
                    nii.hdr.srow_x(2)*cut_from_P + ...
                    nii.hdr.srow_x(3)*cut_from_I;
nii.hdr.srow_y(4) = nii.hdr.srow_y(4) + ...
                    nii.hdr.srow_y(1)*cut_from_L + ...
                    nii.hdr.srow_y(2)*cut_from_P + ...
                    nii.hdr.srow_y(3)*cut_from_I;
nii.hdr.srow_z(4) = nii.hdr.srow_z(4) + ...
                    nii.hdr.srow_z(1)*cut_from_L + ...
                    nii.hdr.srow_z(2)*cut_from_P + ...
                    nii.hdr.srow_z(3)*cut_from_I;
                
% Save into NIFTI file with suffix _crop
nii_tool('save',nii,[strrep(strrep(filename,'.nii.gz',''),'.nii','') '_crop.nii'])