» scaled=xmr(bold(:,:,:),0,0,0,4,4,1,0,0,0); %scale up bold
» scaled(find(scaled<300)) =0; %remove voxels darker than 300
» for i=1:64, funcEd(:,:,i)=double(edge(scaled(:,:,i),50,'sobel')); end %find edge and name it funcEd
» Ranat=xmr(anat,-5,-4,0,1,1,1,0,0,0); %rotate anat and name in Ranat

function mod_reorient(PP,hold) 
% Re-orient images using .mat file
% FORMAT mod_reorient(V,hold);
% V      -  is a memory mapped image volume; if not specified, spm 
%           user interface opens for user to select image file.  
% hold   -  sets the interpolation method for the resampling, (default=-9)
%           0          Zero-order hold (nearest neighbour).
%           1          First-order hold (trilinear interpolation).
%           2->127     Higher order Lagrange (polynomial) interpolation using
%                      different holds (second-order upwards).
%          -127 - -1   Different orders of sinc interpolation.
%
%_______________________________________________________________________
%
% The function reslices the input images. 
% Output images (with the prefix "r") are written in the transverse 
% orientation (using information from the ".mat" files). 
%_______________________________________________________________________ 

% John Ashburner %E%
%
%modified by Jason Steffener
%Modification involves reslicing images in their native 
%voxel size and dimensions.
%Note this program now resets the origin back to the center
%of the image.
%This now interpolates using a 9x9x9 sinc window
% 
% Modified by Josh Bizzell for BIAC, 2003-May-21
% Added HOLD input argument.
% Changed so slices match up with original image.

if nargin<1, 
  PP = spm_get(Inf,'*.img','Select file to reorient'); 
  hold = -9;
end; 
if nargin<2, 
  if iscellstr(PP) | isstr(PP), hold = -9; 
  elseif isint(PP)
    hold = PP;
    PP = spm_get(Inf,'*.img','Select file to reorient');
  end
end
VV = spm_vol(PP);
for V=VV', 
  mn=V.dim(1:3)/(-2);
  vox = spm_imatrix(V.mat); 
  vox = vox(7:9);
  mat = spm_matrix([0 0 0 0 0 0 vox])*spm_matrix([mn]); 
  dim=V.dim(1:3);
  VO = V; 
  [lpath,name,ext] = fileparts(V.fname); 
  VO.fname = fullfile(lpath,['r' name ext]); 
  VO.dim(1:3) = dim(1:3); 
  VO.mat = mat;
  spm_progress_bar('Init',dim(3),'reslicing...','planes completed'); 
  VO = spm_create_image(VO); 
  for i=1:dim(3), 
    M = inv(spm_matrix([0 0 -i])*inv(VO.mat)*V.mat); 
    img = spm_slice_vol(V,M,dim(1:2),hold); %The -9 represents sinc
    spm_write_plane(VO,img,i);              %interpolation with a 
    spm_progress_bar('Set',i)               %9x9x9 window.	
  end; 
  spm_progress_bar('Clear'); 
end;
return;

M = inv(spm_matrix([0 0 -i])*inv(VO.mat)*V.mat);