function view_slices(input_file, input_thresh, mask_file, mask_thresh, slices, frame)

%VIEW_SLICES displays the slices in a 3D volume.
%
% VIEW_SLICES( INPUT_FILE [, MASK_FILE [, MASK_THRESH [, SLICES [, FRAME]]]])
%
% INPUT_FILE is the name of a single image file with multiple frames. 
% Coordinates are in voxels, starting at 0, as in 'register'. Since matlab 
% can't reverse axis labels, they are negative if the step sizes are negative 
% - ignore the minus signs.
%
% MASK_FILE is a mask file. If empty, it is ignored. Default is [].
%
% MASK_THRESH defines the search volume as the first frame of MASK_FILE 
% > MASK_THRESH. If MASK_THRESH is a vector [a b], a<=b, then mask 
% is a < MASK_FILE <= b. Default is 0. 
%
% SLICES is a vector of desired slices starting at 0, as in 'register',
% displayed in the top left. If SLICES is a single slice, then axis values
% are given in voxels, starting at 0, as in 'register'. Since matlab 
% can't reverse axis labels, they are negative if the step sizes are negative 
% - ignore the minus signs. Default is 0:numslices-1, i.e. all the slices.
%
% FRAME is the desired frame number. Default is 1.

%############################################################################
% COPYRIGHT:   Copyright 2002 K.J. Worsley, 
%              Department of Mathematics and Statistics,
%              McConnell Brain Imaging Center, 
%              Montreal Neurological Institute,
%              McGill University, Montreal, Quebec, Canada. 
%              worsley@math.mcgill.ca
%
%              Permission to use, copy, modify, and distribute this
%              software and its documentation for any purpose and without
%              fee is hereby granted, provided that this copyright
%              notice appears in all copies. The author and McGill University
%              make no representations about the suitability of this
%              software for any purpose.  It is provided "as is" without
%              express or implied warranty.
%############################################################################

% Defaults:

if nargin < 2
   mask_file=[]
end
if nargin < 3
   mask_thresh=0
end
if nargin < 5
   frame=1
end

d=fmris_read_image(input_file,0,0);
numslices=d.dim(3)
numys=d.dim(2)
numxs=d.dim(1)
ext=input_file((length(input_file)-2):length(input_file));
isanalyze= all(ext=='img')

if nargin < 4
   slices=(1:numslices)-1
end

if ~isempty(mask_file)
   mask_thresh1=mask_thresh(1);
   if length(mask_thresh)>=2
      mask_thresh2=mask_thresh(2);
   else
      mask_thresh2=Inf;
   end
   m=fmris_read_image(mask_file,slices+1,1);
   m.data= (m.data>mask_thresh1 & m.data<=mask_thresh2);
   xf=find(max(max(m.data,[],2),[],3));
   xr=min(xf):max(xf);
   yf=find(max(max(m.data,[],1),[],3));
   yr=min(yf):max(yf);
else
   xr=1:numxs;
   yr=1:numys;
end

nx=length(xr);
ny=length(yr);
nslices=length(slices);
if nslices>1
   mx=ceil(sqrt(nx*ny*nslices)/nx);
   my=ceil(nslices/mx);
   M=zeros(mx*nx,my*ny).*NaN;
   for i=1:mx
      for j=1:my
         islice=i+(my-j)*mx;
         if islice<=nslices
            slice=slices(islice)+1;
            d=fmris_read_image(input_file,slice,frame);
            v=d.data(xr,yr);
            if ~isempty(mask_file)
               v(m.data(xr,yr,islice)==0)=mask_value;
            end
            if d.vox(1)<0 & isanalyze
               v=flipdim(v,1);
            end
            if d.vox(2)<0 & isanalyze
               v=flipdim(v,2);
            end
            M((i-1)*nx+(1:nx),(j-1)*ny+(1:ny))=v;
         end
      end
   end
   M(isnan(M))=min(min(M));
   imagesc(M'); axis xy; axis off; colorbar;
   title([input_file ', frame ' num2str(frame)]);
   
   for i=1:mx
      for j=1:my
         islice=i+(my-j)*mx;
         if islice<=nslices
            slice=slices(islice);
            text((i-1)*nx+nx*.05,(j-1)*ny+ny*.9,num2str(slice),'Color','w');
         end
      end
   end
else
   d=fmris_read_image(input_file,slices+1,frame);
   v=d.data(xr,yr);
   if ~isempty(mask_file)
      v(m.data(xr,yr,1)==0)=mask_value;
   end
   if d.vox(1)<0 & isanalyze
      v=flipdim(v,1);
   end
   if d.vox(2)<0 & isanalyze
      v=flipdim(v,2);
   end
   if d.vox(1)>0 
      xr=xr-1;
      xlab='x';
   else
      xr=-(d.dim(1)-xr);
      xlab='-x';
   end
   if d.vox(2)>0 
      yr=yr-1;
      ylab='y';
   else
      yr=-(d.dim(2)-yr);
      ylab='-y';
   end
   v(isnan(v))=min(min(v));
   imagesc(xr,yr,v'); axis xy; grid on; xlabel(xlab); ylabel(ylab); colorbar;
   title([input_file ', slice ' num2str(slices) ', frame ' num2str(frame)]);
end

return


input_file='c:/keith/results/ha_100326_hmw_mag_t.mnc';
mask_file='c:/keith/data/brian_ha_19971124_1_100326_mri_MC.mnc';
mask_thresh=fmri_mask_thresh(mask_file);

plot([1 2])
text(1.5,1.5,'h','Color','r');
i=1
j=1

viewslices(input_file, mask_file, mask_thresh, slices, frame)  
viewslices(input_file, mask_file, mask_thresh,1:5)  
viewslices(input_file, mask_file, mask_thresh)  
viewslices(mask_file, mask_file, mask_thresh,1:3)