NAME¶

m-anlz - Analyze (SPM) medical image format (MedCon)

DESCRIPTION¶

This is a very simple format. The basic headers are written in one file with extension `.hdr', the image data in another file with extension `.img'.

The basic defines for the format:

---------------------------------------------------------------------------
typedef struct Header_Key_t{


        Int32  sizeof_hdr;               /* 348 or 148                 */


        char data_type[10];              /* "dsr"                      */


        char db_name[18];                /* filename without extension */


        Int32 extents;                   /* 16384                      */


        Int16 session_error;


        char regular;                    /* 'r'                        */


        char hkey_un0;
} MDC_ANLZ_HEADER_KEY;
#define MDC_ANLZ_HK_SIZE 40 
typedef struct Image_Dimensions_t{


        Int16 dim[8];                    /* [0] = # of dimensions      */


                                         /* [1] = X-dim                */


                                         /* [2] = Y-dim                */


                                         /* [3] = Z-dim                */


                                         /* [4] = t-dim                */


                                         /* ...                        */


        Int16 unused[7];


        Int16 datatype;                  /* pixel type                 */


                                         /*  0 = Unknown   1 = one-bit */


                                         /*  2 = Uint8     4 = Int16   */


                                         /*  8 = Int32    16 = float   */


                                         /* 32 = complex  64 = double  */


                                         /*128 = RGB     255 = all     */


        Int16 bitpix;                    /* bits per pixel             */


        Int16 dim_un0;


        float pixdim[8];                 /* [0] = # of dimensions      */


                                         /* [1] = X-dim (mm)           */


                                         /* [2] = Y-dim (mm)           */


                                         /* [3] = Z-dim (mm)           */


                                         /* [4] = t-dim (ms)           */


                                         /* ...                        */


        float funused[6];


        float compressed;


        float verified;


        Int32 glmax,glmin;
} MDC_ANLZ_IMAGE_DIMS;
#define MDC_ANLZ_IMD_SIZE 108
typedef struct Data_History_t{


        char descrip[80];


        char aux_file[24];


        char orient;                     /* patient orientation        */


                                         /* 0 = transverse unflipped   */


                                         /* 1 = coronal unflipped      */


                                         /* 2 = sagittal unflipped     */


                                         /* 3 = transverse flipped     */


                                         /* 4 = coronal flipped        */


                                         /* 5 = sagittal flipped       */


        char originator[10];


        char generated[10];


        char scannum[10];


        char patient_id[10];


        char exp_date[10];


        char exp_time[10];


        char hist_un0[3];


        Int32 views;


        Int32 vols_added;


        Int32 start_field;


        Int32 field_skip;


        Int32 omax, omin;


        Int32 smax, smin;
} MDC_ANLZ_DATA_HIST;
#define MDC_ANLZ_DH_SIZE 200
---------------------------------------------------------------------------

The structures are defined in the order as they should be found in the file. The Data_History header is not obliged. The SPM Analyze format, intended for the SPM software, differs a little from the normal Analyze format.

What does the format support or not support:

===========================================================================
Item            Supported                             Not Supported
===========================================================================
Color Map     : grayscale                                   -
File Endian   : little & big                                - 
Pixeltypes    : 1-bit, Uint8, Int16, Int32           Int8,Uint16,Uint32


                float, double, (complex)               Int64,Uint64
===========================================================================
Scaling factors  : quantify & calibrate factors/image  are NOT supported
---------------------------------------------------------------------------
Dimensions/Image : different dimensions for each image are NOT supported
---------------------------------------------------------------------------
Pixeltypes/Image : different pixeltypes for each image are NOT supported
---------------------------------------------------------------------------
SPM remarks      : 1) imd.funused[0] = the offset 


                   2) imd.funused[1] = one global scaling factor


                   3) (Int16)dh.originator[0...1] \


                      (Int16)dh.originator[2...3]  } =  origin (X, Y, Z)


                      (Int16)dh.originator[4...5] / 
===========================================================================

NOTES¶

A note about the image (patient) orientation in SPM:

X-axis

increases from leftside (hand) to rightside (hand).

Y-axis

increases from posterior (back) to anterior (front).

Z-axis

increases from inferior (feet) to superior (head).

FILES¶

/usr/local/xmedcon/source/m-anlz.h      The header file.
/usr/local/xmedcon/source/m-anlz.c      The source file.

SEE ALSO¶

medcon(1), xmedcon(1), xmedcon-config(1)

m-acr(4), m-gif(4), m-inw(4), m-intf(4), m-ecat(4)

medcon(3)

AUTHOR¶

(X)MedCon project was originally written by Erik Nolf (eNlf) for the former PET-Centre at Ghent University (Belgium).