importvtcfromanalyze.m

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

function vtc = importvtcfromanalyze(imgs, bbox, res, imeth)
% importvtcfromanalyze  - import a VTC from Analzye files
%
% FORMAT:       vtc = importvtcfromanalyze(imgs [, bbox [, res [, imeth]])
%
% Input fields:
%
%       imgs        cell array with HDR filenames for BVQXfile
%       bbox        optional 2x3 bounding box (default: auto detect)
%       res         optional resolution (default: Analyze resolution
%                   if 3 or 2, otherwise take best guess)
%       imeth       interpolation, {'linear'}, 'cubic', 'spline'
%
% Output fields:
%
%       vtc         created VTC object

% Version:  v0.7b
% Build:    7090522
% Date:     Sep-05 2007, 10:19 PM CEST
% Author:   Jochen Weber, Brain Innovation, B.V., Maastricht, NL
% URL/Info: http://wiki.brainvoyager.com/BVQXtools

% argument check
if nargin < 1 || ...
   ~iscell(imgs) || ...
    numel(imgs) < 3 || ...
   ~ischar(imgs{1}) || ...
    isempty(imgs{1}) || ...
    exist(imgs{1}(:)', 'file') ~= 2
    error( ...
        'BVQXtools:BadArgument', ...
        'Bad input argument.' ...
    );
end
imgs = imgs(:);
nimg = numel(imgs);
himg = cell(1, nimg);
vimg = zeros(20, nimg);
try
    pbar = BVQXprogress;
    BVQXprogress(pbar, 'setposition', [80, 200, 640, 36]);
    BVQXprogress(pbar, 'settitle', 'Converting Analyze to VTC...');
    BVQXprogress(pbar, 0, 'Checking HDRs...', 'visible', 0, 8 * nimg);
catch
    pbar = [];
end
try
    for ic = 1:nimg
        if ~ischar(imgs{ic}) || ...
            isempty(imgs{ic})
            error('BAD_IMAGENAME');
        end
        himg{ic} = BVQXfile(imgs{ic});
        if numel(himg{ic}) ~= 1 ||...
           ~isBVQXfile(himg{ic}, 'hdr')
            error('BAD_IMAGECONT');
        end
        icf = himg{ic}.CoordinateFrame;
        vimg(:, ic) = [icf.Trf(:); icf.Dimensions(:)];
        if ~isempty(pbar)
            BVQXprogress(pbar, ic);
        end
    end
    if any(any(diff(vimg, 1, 2)))
        error( ...
            'BVQXtools:BadArgument', ...
            'Spatial orientation/dimensions mismatch between images.' ...
        );
    end
catch
    clearbvqxobjects(himg);
    if ~isempty(pbar)
        closebar(pbar);
    end
    error( ...
        'BVQXtools:BadArgument', ...
        'Error loading image %d.', ...
        ic ...
    );
end
bb = himg{1}.BoundingBox;
sfn = himg{1}.FilenameOnDisk;
if nargin < 2 || ...
   ~isa(bbox, 'double') || ...
   ~isequal(size(bbox), [2, 3]) || ...
    any(isnan(bbox(:)) | bbox(:) < 0 | bbox(:) > 255)
    bbox = bb.BBox;
else
    bbox = round(bbox);
end
if nargin < 3 || ...
   ~isa(res, 'double') || ...
    numel(res) ~= 1 || ...
   ~any((1:12) == res)
    if all(bb.ResXYZ == bb.ResXYZ(1))
        if any((1:12) == bb.ResXYZ(1))
            res = bb.ResXYZ(1);
            imeth = 'nearest';
        else
            res = ceil(bb.ResXYZ(1) / 2);
        end
    else
        res = ceil(min(bb.ResXYZ) / 2);
    end
end
if nargin < 4 || ...
   ~ischar(imeth) || ...
   ~any(strcmpi(imeth(:)', {'cubic', 'linear', 'nearest', 'spline'}))
    imeth = 'linear';
else
    imeth = lower(imeth(:)');
end

% build coordinate indices for sampling
xs = 0.5 * res + (bbox(1, 1):res:bbox(2, 1));
ys = 0.5 * res + (bbox(1, 2):res:bbox(2, 2));
zs = 0.5 * res + (bbox(1, 3):res:bbox(2, 3));

% create VTC data
vtd = uint16([]);
vtd(nimg, numel(xs), numel(ys), numel(zs)) = 0;
vts = size(vtd);

% guess scaling
himg{1}.VoxelData = himg{1}.VoxelData(:, :, :);
vds = single(himg{1}.VoxelData);
vdm = max(vds(:));
if vdm > 16384
    vdf = single(16384 / vdm);
else
    vdf = [];
end

% interpolation
[xs, ys, zs] = ndgrid(single(xs), single(ys), single(zs));
xs = xs(:);
ys = ys(:);
zs = zs(:);
c = 128 - [zs, xs, ys];
if ~isempty(pbar)
    BVQXprogress(pbar, nimg, 'Sampling images...');
end
for ic = 1:nimg
    try
        himg{ic}.VoxelData = himg{ic}.VoxelData(:, :, :);
        hy = reshape(himg{ic}.SampleCoords(c, 1, imeth, 'tal'), [1, vts(2:4)]);
        himg{ic}.ClearObject;
        himg{ic} = [];
        if ~isempty(vdf)
            hy = vdf * hy;
        end
        if ~isempty(pbar)
            BVQXprogress(pbar, nimg + 7 * ic);
        end
        vtd(ic, :, :, :) = hy;
    catch
        if ~isempty(pbar)
            closebar(pbar);
        end
        error( ...
            'BVQXtools:InternalError', ...
            'Error sampling data of volume %d.', ...
            ic ...
        ),
    end
end

% create VTC
vtc = bless(BVQXfile('new:vtc'), 1);
vtc.NameOfSourceFMR = sfn;
vtc.Resolution = res;
vtc.XStart = bbox(1, 1);
vtc.XEnd = bbox(1, 1) + res * vts(2);
vtc.YStart = bbox(1, 2);
vtc.YEnd = bbox(1, 2) + res * vts(3);
vtc.ZStart = bbox(1, 3);
vtc.ZEnd = bbox(1, 3) + res * vts(4);
vtc.VTCData = vtd;
vtd = [];
clear vtd;
vtc.NrOfVolumes = size(vtc.VTCData, 1);