trackfile_headers.h

Go to the documentation of this file.

/******************************************************************************
 * Copyright 2014 Micah C Chambers (micahc.vt@gmail.com)
 *
 * NPL is free software: you can redistribute it and/or modify it under the
 * terms of the BSD 2-Clause License available in LICENSE or at
 * http://opensource.org/licenses/BSD-2-Clause
 *
 ******************************************************************************/

#ifndef TRACKFILE_HEADERS_H
#define TRACKFILE_HEADERS_H

//id_string[6]    char 6       ID string for track file. The first 5
//                             characters must be "TRACK".
//dim[3]          short int    Dimension of the image volume.
//voxel_size[3]   float        Voxel size of the image volume.
//origin[3]       float        Origin of the image volume. This field is not yet
//                             being used by TrackVis. That means the origin is
//                             always (0, 0, 0).
//n_scalars    short int 2     Number of scalars saved at each track point
//                             (besides x, y and z coordinates).
//scalar_name[10][20] char     Name of each scalar. Can not be longer than
//                             20 characters each.
//n_properties    short int    Number of properties saved at each track.
//property_name[10][20] char   Name of each property. Can not be longer than
//                             20 characters each. Can only store up to 10 names.
//vox_to_ras[4][4] float       4x4 matrix for voxel to RAS (crs to xyz)
//                             transformation. If vox_to_ras[3][3] is 0, it
//                             means the matrix is not recorded. This field is
//                             added from version 2.
//reserved[444]    char        Reserved space for future version.
//voxel_order[4]   char        Storing order of the original image data. Explained here.
//pad2[4]    char 4            Paddings.
//image_orientation_patient[6] float 24 Image orientation of the original image.
//                             As defined in the DICOM header.
//pad1[2]    char 2            Paddings.
//invert_x   unsigned char    1 Inversion/rotation flags used to generate
//           this track file. For internal use only.
//invert_y   unsigned char 1 As above.
//invert_z   unsigned char 1 As above.
//swap_xy    unsigned char 1 As above.
//swap_yz    unsigned char 1 As above.
//swap_zx    unsigned char 1 As above.
//n_count    int 4             Number of tracks stored in this track file.
//                             0 means the number was NOT stored.
//version    int 4             Version number. Current version is 1.
//hdr_size    int 4            Size of the header. Used to determine byte swap.
//                             Should be 1000.
//<---------------------BODY-------------------------->
//From Experience these coordinates are index*spacing
//
//Track #1    int 4            Number of points in this track, as m.
//        float (3+n_s)*4      Track Point #1. Contains 3 plus n_s float
//                             numbers. First 3 float numbers are the
//                             x/y/z coordinate of this track point,
//                             followed by n_s float numbers representing
//                             each of its scalars.
//        float(3+n_s)*4       Track Point #2. Same as above.
//...    ...     ...
//        float(3+n_s)*4       Track Point #m. Same as above.
//        float    n_p*4       n_p float numbers representing each
//                             of the properties of this track.
//Track #2     Same as above.
//
//...          Same as above.
//
//Track #n     Same as above.

typedef struct
{
    char id_string[6];

    short int dim[3];
    float voxel_size[3];
    float origin[3];

    short int n_scalars;
    char scalar_name[10][20];

    short int n_properties;
    char property_name[10][20];

    float vox_to_ras[4][4];

    char reserved[444];

    char voxel_order[4];
    char padA4[4];
    float image_orientation_patient[6];
    char padB2[2];

    unsigned char invert_x;
    unsigned char invert_y;
    unsigned char invert_z;
    unsigned char swap_xy;
    unsigned char swap_yz;
    unsigned char swap_zx;

    int n_count;
    int version;
    int hdr_size; //shouldbe 1000

    unsigned char data[0];
} TrkHead;

/* reads a Brainsuite .dft file */
//0 magic   char[8] An 8 character string designating the filetype
//                  (‘DFC_LE\0\0′ or ‘DFC_BE\0\0′*).
//8 version uint8[4]    4 unsigned characters, representing the version number
//                  (e.g., 1.0.0.2)
//12    header size int32   size of the stored header
//16    data start  int32   offset from beginning of file to where the curves
//                          are stored
//20    metadata offset int32   offset from beginning of file to where the
//                          metadata are stored
//24    subject data offset int32   offset from beginning of file to where the
//                          subject data are stored (not currently used)
//28    # of contours   int32   number of curves stored in file
//32    # of seedpoints int64   number of seedpoints stored in file
//Cuve0 Curve1  …  CurveNC-1
//
//N x0  y0  z0  x1  y1  z1  …  xN-1    yN-1    zN-1

typedef struct
{
    char id_string[8];  // "DFT_LE  "
    uint8_t version[4];
    int32_t header_size;
    int32_t data_start;
    int32_t metadata_offset;
    int32_t subject_data_offset;
    int32_t num_contours;
    int64_t seedpoints;
    char padding[24];
} DftHead;

#endif //TRACKFILE_HEADERS_H
#define TRACKS_H