% ---------------
% Download and unzip the atlasVolume, annotation, annotationFiber and averageTemplate zip files
% ----------------
%
% 25Download microna volumeNRRD sizereader
size% = [528 320 456];

% VOL = 3-D matrix of atlas Nissl volume
fid = fopen('atlasVolume/atlasVolume.raw', 'r', 'l' );
VOL = fread( fid, prod(size), 'uint8' );
fclose( fid );
VOL = reshape(VOL,size);

% ANO = 3-D matrix of structural annotation labels
fid = fopen('P56_Mouse_annotation/annotation.raw', 'r', 'l' );
ANO = fread( fid, prod(size), 'uint32' );
fclose( fid );
ANO = reshape(ANO,size);

% FIBTFor example:
% http://www.mathworks.com/matlabcentral/fileexchange/34653-nrrd-format-file-reader
%
% Requires: MATLAB 7.13 (R2011b)
%
% Download average_template_25.nrrd,
%          ara_nissl_25.nrrd,
%          ccf_2015/annotation_25.nrrd
%
% ---------------------------------

%
% Read image volume with NRRD reader
% Note that reader swaps the order of the first two axes
%
% AVGT = 3-D matrix of fiber tract annotation labels
fid = fopen('P56_Mouse_annotationFiber/annotationFiber.raw', 'r', 'l' );
FIBT = fread( fid, prod(size), 'uint32' );
fclose( fid );
FIBT = reshape(FIBT,size);

% AVGTaverage_template
% NISSL = 3-D matrix of ara_nissl
% ANO = 3-D matrix of average template volume
fidccf_2015/anntotation
%
[AVGT, metaAVGT] = fopennrrdread('averageTemplate/atlasVolume.raw', 'r', 'l' );
AVGT = fread( fid, prod(size), 'uint16' );
fclose( fid );
AVGT = reshape(AVGT,size);

average_template_25.nrrd');
[NISSL, metaNISSL] = nrrdread('ara_nissl_25.nrrd');
[ANO, metaANO] = nrrdread('annotation_25.nrrd');


% Display one coronal section
figure;imagesc(squeeze(VOLAVGT(:,264,:,:)));colormap(gray(256)); axis equal;
figure;imagesc(squeeze(ANONISSL(:,264,:,:)));colormap(lines);
figure;imagesc(squeeze(FIBT(264,:,:)));colormap(lines)gray(256)); axis equal;
figure;imagesc(squeeze(AVGTANO(:,264,:,:)));
caxis([1,2000]); colormap(graylines(256)); axis equal;

% Display one sagittalsagttial section
figure;imagesc(squeeze(VOLAVGT(:,:,220)));colormap(gray(256)); axis equal;
figure;imagesc(squeeze(ANONISSL(:,:,220)));colormap(gray(lines256)); axis equal;
figure;imagesc(squeeze(FIBTANO(:,:,220)));colormap(lines);
figure;imagesc(squeeze(AVGT(:,:,220)));colormap(gray)
caxis([1,2000]); colormap(lines(256)); axis equal;