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# read_ctf_mri

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

### Function Synopsis

    [Cube,Header] = read_ctf_mri(MRIfile,MACHINEFORMAT);

### Help Text

    READ_CTF_MRI - Read CTF MRI format (Version 2.1)
     function [Cube,Header] = read_ctf_mri(MRIfile,MACHINEFORMAT);
    function [Cube,Header] = read_ctf_mri(MRIfile);
     MRIfile is a valid /mri file name
     Cube is a 256x256xN volume of MR scans
     Header reproduced the Header MR structure from CTF file format

     function [Cube,Header] = read_ctf_mri(MRIfile,MACHINEFORMAT);
     MACHINEFORMAT is an optional string that specifies the machine format for data storage
     'l' is for little endian
     'b' stands for big endian (Default)

     CTF MRI File Version 2.1
     The CTF MRI File format used by MRIViewer consists of a binary file with a
     1,028 byte header. The MRI data can be in 8-bit (unsigned character) or 16-bit
     (unsigned short integer) format and consists of 256 x 256 pixel slices, stored as
     256 contiguous sagittal slices from left to right (or right to left if head orientation
     is "left-on-right"). Each slice is stored as individual pixels starting at the
     top left corner and scanning downwards row by row. Therefore the coronal
     position is fastest changing, axial position second fastest changing and sagittal
     position slowest changing value in the file, always in the positive direction for
     each axis (see section on Head Coordinate System for axis definitions). By
     default CTF MRI files have the file extension ".mri"

### Cross-Reference Information

This function is called by

    bst_mriviewer                      C:\BrainStorm_2001\Toolbox\bst_mriviewer.m

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

    function [Cube,Header] = read_ctf_mri(MRIfile,MACHINEFORMAT);
    %READ_CTF_MRI - Read CTF MRI format (Version 2.1)
    % function [Cube,Header] = read_ctf_mri(MRIfile,MACHINEFORMAT);
    %function [Cube,Header] = read_ctf_mri(MRIfile);
    % MRIfile is a valid /mri file name
    % Cube is a 256x256xN volume of MR scans
    % Header reproduced the Header MR structure from CTF file format
    %
    % function [Cube,Header] = read_ctf_mri(MRIfile,MACHINEFORMAT);
    % MACHINEFORMAT is an optional string that specifies the machine format for data storage
    % 'l' is for little endian
    % 'b' stands for big endian (Default)
    %
    % CTF MRI File Version 2.1
    % The CTF MRI File format used by MRIViewer consists of a binary file with a
    % 1,028 byte header. The MRI data can be in 8-bit (unsigned character) or 16-bit
    % (unsigned short integer) format and consists of 256 x 256 pixel slices, stored as
    % 256 contiguous sagittal slices from left to right (or right to left if head orientation
    % is "left-on-right"). Each slice is stored as individual pixels starting at the
    % top left corner and scanning downwards row by row. Therefore the coronal
    % position is fastest changing, axial position second fastest changing and sagittal
    % position slowest changing value in the file, always in the positive direction for
    % each axis (see section on Head Coordinate System for axis definitions). By
    % default CTF MRI files have the file extension ".mri"

    %<autobegin> ---------------------- 26-May-2004 11:34:13 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Utility - General
    %
    % At Check-in: $Author: Mosher $  $Revision: 6 $  $Date: 5/26/04 10:02a $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 24-May-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> ------------------------ 26-May-2004 11:34:13 -----------------------

    % MRIViewer uses these cardinal directions as axes in an internal coordinate system
    % where sagittal = X, coronal = Y and axial = Z forming an additional
    % right-handed coordinate system which is translated and rotated with respect to
    % the Head Coordinate System and has its origin at the upper left anterior corner
    % of the volume.

    % /---Script Authors-------------------------------------\
    % |  *** Sylvain Baillet, Ph.D.                          |
    % |  Cognitive Neuroscience & Brain Imaging Laboratory   |
    % |  CNRS UPR640 - LENA                                  |
    % |  Hopital de la Salpetriere, Paris, France            |
    % |  sylvain.baillet@chups.jussieu.fr                    |
    % \------------------------------------------------------/
    %
    % Script History ---------------------------------------------------------------
    % SB  11 Mar-2004 Creation
    % Script History ---------------------------------------------------------------

    if nargin == 1
        MACHINEFORMAT = 'b';
    end

    file = fopen(MRIfile,'rb',MACHINEFORMAT);
    if file < 1
        errordlg(['Error when opening : ',fullfile(pwd,MRIfile)]);
        return
    end

    Header.identifierString = char(fread(file,32,'char')');
    Header.imageSize = fread(file,1,'short');
    Header.dataSize = fread(file,1,'short');
    Header.clippingRange = fread(file,1,'short');
    Header.imageOrientation= fread(file,1,'short');
    Header.mmPerPixel_sagittal = fread(file,1,'float32');
    Header.mmPerPixel_coronal = fread(file,1,'float32');
    Header.mmPerPixel_axial = fread(file,1,'float32');

    % Head Model Info
    Header.HeadModel_Info.Nasion_Sag = fread(file,1,'short');
    Header.HeadModel_Info.Nasion_Cor = fread(file,1,'short');
    Header.HeadModel_Info.Nasion_Axi = fread(file,1,'short');
    Header.HeadModel_Info.LeftEar_Sag = fread(file,1,'short');
    Header.HeadModel_Info.LeftEar_Cor = fread(file,1,'short');
    Header.HeadModel_Info.LeftEar_Axi = fread(file,1,'short');
    Header.HeadModel_Info.RightEar_Sag = fread(file,1,'short');
    Header.HeadModel_Info.RightEar_Cor = fread(file,1,'short');
    Header.HeadModel_Info.RightEar_Axi = fread(file,1,'short');
    Header.HeadModel_Info.defaultSphereX= fread(file,1,'float32');
    Header.HeadModel_Info.defaultSphereY= fread(file,1,'float32');
    Header.HeadModel_Info.defaultSphereZ= fread(file,1,'float32');
    Header.HeadModel_Info.defaultSphereRadius= fread(file,1,'float32');
    % Head Model Info ********************************************

    % Image Info
    Header.Image_Info.modality = fread(file,1,'short');
    Header.Image_Info.manufacturerName = fread(file,64,'char');
    Header.Image_Info.instituteName = fread(file,64,'char');
    Header.Image_Info.patientID = fread(file,32,'char');
    Header.Image_Info.dateAndTime = fread(file,32,'char');
    Header.Image_Info.scanType = fread(file,32,'char');
    Header.Image_Info.contrastAgent = fread(file,32,'char');
    Header.Image_Info.imagedNucleus = fread(file,32,'char');
    Header.Image_Info.Frequency = fread(file,1,'float32');
    Header.Image_Info.FieldStrengh = fread(file,1,'float32');
    Header.Image_Info.EchoTime = fread(file,1,'float32');
    Header.Image_Info.RepetitionTime = fread(file,1,'float32');
    Header.Image_Info.InversionTime = fread(file,1,'float32');
    Header.Image_Info.FlipAngle = fread(file,1,'float32');
    Header.Image_Info.NoExcitations = fread(file,1,'short');
    Header.Image_Info.NoAcquisitions = fread(file,1,'short');
    Header.Image_Info.commentString = fread(file,256,'char');
    Header.Image_Info.forFutureUse = fread(file,64,'char');
    % Image Info ********************************************

    Header.headOrigin_sagittal = fread(file,1,'float32');
    Header.headOrigin_coronal = fread(file,1,'float32');
    Header.headOrigin_axial  = fread(file,1,'float32');

    Header.rotate_coronal = fread(file,1,'float32');
    Header.headOrigin_sagittal = fread(file,1,'float32');
    Header.headOrigin_axial  = fread(file,1,'float32');
    Header.orthogonalFlag = fread(file,1,'short');
    Header.unused = fread(file,272,'uchar');

    fseek(file,1028,-1); % Skip the whole header by padding to 1028

    % Header Info  ********************************************

    %Read Image

    tmpString = {'uchar','ushort'};

    try
        dataClass = tmpString{Header.dataSize};
    catch
        errordlg('Unrecognized data format - Please check the file format');
        return
    end

    Cube = int16(fread(file, prod([256 256 Header.imageSize]),dataClass)); % Read the whole volume / store in a huge vector
    fclose(file);
    Cube = reshape(Cube,256,256,Header.imageSize); % reshape it into a 3-D array.

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