fmr_createamr.m

toolbox of BVQX, This is the access between BV and matlab. It will help you to analysis data from BV

function amr = fmr_CreateAMR(hfile, opts)
% FMR::CreateAMR  - generate an AMR file
%
% FORMAT:       amr = fmr.CreateAMR([opts]);
%
% Input fields:
%
%       opts        optional struct with settings
%        .autoctr   auto contrast, default: false
%        .invert    invert intensities, default: true
%        .thresh    threshold, default: 0
%        .vol       1x1 or 1xN array with volumes to sample, default: 1
%
% Note: as the FMR object is NOT returned, the AMR reference is NOT set!

% Version:  v0.7b
% Build:    7083009
% Date:     Aug-30 2007, 9:33 AM CEST
% Author:   Jochen Weber, Brain Innovation, B.V., Maastricht, NL
% URL/Info: http://wiki.brainvoyager.com/BVQXtools

% argument check
if nargin < 1 || ...
    numel(hfile) ~= 1 || ...
   ~isBVQXfile(hfile, 'fmr')
    error( ...
        'BVQXfile:BadArgument', ...
        'Invalid call to %s.', ...
        mfilename ...
    );
end
bc = bvqxfile_getcont(hfile.L);
if nargin < 2 || ...
   ~isstruct(opts) || ...
    numel(opts) ~= 1
    opts = struct;
end
if ~isfield(opts, 'autoctr') || ...
    numel(opts.autoctr) ~= 1 || ...
   ~islogical(opts.autoctr)
    opts.autoctr = false;
end
if ~isfield(opts, 'dim') || ...
    numel(opts.dim) ~= 2 || ...
   ~isa(opts.dim, 'double') || ...
    any(isnan(opts.dim) | opts.dim < 64 | opts.dim > 512 | ...
        opts.dim ~= fix(opts.dim))
    opts.dim = [256, 256];
else
    opts.dim = 2 * round(opts.dim(:)' / 2);
end
if ~isfield(opts, 'invert') || ...
    numel(opts.invert) ~= 1 || ...
   ~islogical(opts.invert)
    opts.invert = true;
end
if ~isfield(opts, 'thresh') || ...
    numel(opts.thresh) ~= 1 || ...
   ~isa(opts.thresh, 'double') || ...
    isnan(opts.thresh) || ...
    opts.thresh < 0 || ...
    opts.thresh > 32767
    opts.thresh = uint16(0);
else
    opts.thresh = uint16(floor(opts.thresh));
end
if ~isfield(opts, 'vol') || ...
    isempty(opts.vol) || ...
   ~isa(opts.vol, 'double') || ...
    any(isnan(opts.vol(:)) | opts.vol(:) < 1 | ...
        opts.vol(:) > 512 | bc.NrOfVolumes | ...
        opts.vol(:) ~= fix(opts.vol(:)))
    opts.vol = 1;
else
    opts.vols = unique(opts.vol(:)');
end

% make sure data is loaded
try
    if isempty(bc.Slice) || ...
        ~isstruct(bc.Slice) || ...
        ~isfield(bc.Slice, 'STCData')
        fmr_LoadSTC(hfile);
        bc = bvqxfile_getcont(hfile.L);
    end
catch
    error( ...
        'BVQXfile:InternalError', ...
        'Error loading slice data.' ...
    );
end

% get FMR resolution
dmx = bc.ResolutionX;
dmy = bc.ResolutionY;
dmz = bc.NrOfSlices;

% build output
amr = BVQXfile('new:amr');
amrc = bvqxfile_getcont(amr.L);
slc = amrc.Slice(1);

% init slice object
slc.BITMAPFILEHEADER.bfSize      = 1078 + prod(opts.dim);
slc.BITMAPINFOHEADER.bfWidth     = opts.dim(2);
slc.BITMAPINFOHEADER.bfHeight    = opts.dim(1);
slc.BITMAPINFOHEADER.biImageSize = prod(opts.dim);
slc(2:dmz) = slc(1);

% compute interpolation matrix
[s1, s2] = ndgrid( ...
    1 + 0:(opts.dim(1) - 1) / (opts.dim(1) / dmy),  ...
    1 + 0:(opts.dim(2) - 1) / (opts.dim(2) / dmx));

% build data
amrd = zeros([opts.dim, dmz]);

% interpolate data
for sc = 1:dimz
    
    % depends on file version
    if bc.FileVersion < 5 || ...
        bc.DataStorageFormat == 1
        amrd(:, :, sc) = interpn(mean( ...
            bc.Slice(sc).STCData(:, :, opts.vol), 3), s1, s2);
    elseif bc.DataStorageFormat == 2
        amrd(:, :, sc) = interpn(mean( ...
            bc.Slice.STCData(:, :, opts.vol, sc), 3), s1, s2);
    else
        BVQXfile(0, 'clearobj', amr.L);
        error( ...
            'BVQXfile:InvalidObject', ...
            'Unsupported DataStorageFormat.' ...
        );
    end
end

% contrast

% iterate again for storage
for sc = 1:dmz
    
    % store in AMR slice
    slc(sc).AMRData = uint8(round(amrd(:, :, sc)));
end

% fill object
amrc.NrOfSlices = dmz;
amrc.Slice = slc;
bvqxfile_setcont(amr.L, amrc);