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# avw2brainstorm

## (Toolbox/avw2brainstorm.m in BrainStorm 2.0 (Alpha))

### Function Synopsis

    MRI = avw2brainstorm(avw, machine);

### Help Text

    AVW2BRAINSTORM - : Converts an AVW MRI structure (from D. Weber's EEGToolbox) to BRAINSTORM MRI format
     function MRI = avw2brainstorm(avw, machine);
     Reads out an avw structure obtained using the avw_img_read tool from D.
     Weber's EEGToolbox to a BrainStorm MRI structure
     Inputs-
     awv : an AWV structure (see avw_img_read.m in the EEGToolbox)
     machine: is either 'ieee-be' or 'ieee-le' for big and little-endian
     binary data encoding respectively on current machine
     Output:
     MRI : a BrainStorm MRI structure
     See also: avw_img_read.m and help_data_image.m

### Cross-Reference Information

This function calls

    bst_message_window                 C:\BrainStorm_2001\Toolbox\bst_message_window.m

This function is called by

    bst_mriviewer                      C:\BrainStorm_2001\Toolbox\bst_mriviewer.m

### Listing of function C:\BrainStorm_2001\Toolbox\avw2brainstorm.m

    function MRI = avw2brainstorm(avw, machine);
    %AVW2BRAINSTORM - : Converts an AVW MRI structure (from D. Weber's EEGToolbox) to BRAINSTORM MRI format
    % function MRI = avw2brainstorm(avw, machine);
    % Reads out an avw structure obtained using the avw_img_read tool from D.
    % Weber's EEGToolbox to a BrainStorm MRI structure
    % Inputs-
    % awv : an AWV structure (see avw_img_read.m in the EEGToolbox)
    % machine: is either 'ieee-be' or 'ieee-le' for big and little-endian
    % binary data encoding respectively on current machine
    % Output:
    % MRI : a BrainStorm MRI structure
    % See also: avw_img_read.m and help_data_image.m

    %<autobegin> ---------------------- 14-Jun-2004 17:09:45 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Utility - General
    %
    % Alphabetical list of external functions (non-Matlab):
    %   toolbox\bst_message_window.m
    %
    % At Check-in: $Author: Mosher $  $Revision: 3 $  $Date: 6/14/04 3:37p $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 14-Jun-2004
    %
    % Principal Investigators and Developers:
    % ** Richard M. Leahy, PhD, Signal & Image Processing Institute,
    %    University of Southern California, Los Angeles, CA
    % ** John C. Mosher, PhD, Biophysics Group,
    %    Los Alamos National Laboratory, Los Alamos, NM
    % ** Sylvain Baillet, PhD, Cognitive Neuroscience & Brain Imaging Laboratory,
    %    CNRS, Hopital de la Salpetriere, Paris, France
    %
    % See BrainStorm website at http://neuroimage.usc.edu for further information.
    %
    % Copyright (c) 2004 BrainStorm by the University of Southern California
    % This software distributed  under the terms of the GNU General Public License
    % as published by the Free Software Foundation. Further details on the GPL
    % license can be found at http://www.gnu.org/copyleft/gpl.html .
    %
    % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
    % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
    % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
    % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
    % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
    %<autoend> ------------------------ 14-Jun-2004 17:09:45 -----------------------

    % /---Script Author--------------------------------------\
    % |                                                      |
    % | *** Sylvain Baillet, Ph.D.                           |
    % | Cognitive Neuroscience & Brain Imaging Laboratory    |
    % | CNRS UPR640 - LENA                                   |
    % | Hopital de la Salpetriere, Paris, France             |
    % | sylvain.baillet@chups.jussieu.fr                     |
    % \------------------------------------------------------/
    %
    % Date of creation: June 2004

    switch(deblank(avw.hdr.dime.vox_units))
        case 'mm'
            factor = 1;
        case 'm'
            factor = 1000;
        otherwise
            errordlg(sprintf(...
                'Unrecognized ANALYZE voxel units: %s',...
                deblank(avw.hdr.dime.vox_units)))
            return
    end

    MRI.Cube = avw.img;
    MRI.Voxsize = (double(avw.hdr.dime.pixdim([2:4]))*factor);

    MRI.header = 0; % Now for BrainStorm format

    switch double(avw.hdr.dime.bitpix),
        case  1,   precision = 'bit1';
        case  8,   precision = 'uchar';
        case 16,   precision = 'int16';
        case 32,
            if     isequal(avw.hdr.dime.datatype, 8), precision = 'int32';
            else                                      precision = 'single';
            end
        case 64,   precision = 'double';
        otherwise,
            precision = 'uchar';
            bst_message_window('...precision undefined in header, using ''uchar''\n');
    end
    MRI.DataClass = precision;

    switch double(avw.hdr.hist.orient),
        case 0
            MRI.scantype = 'axial';
        case 1
            MRI.scantype = 'coronal';
        case 2
            MRI.scantype = 'sagittal';
    end

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