amide(1) [debian man page]

AMIDE(1)						      General Commands Manual							  AMIDE(1)

NAME

       amide - AMIDE's a Medical Image Data Examiner

SYNOPSIS

       amide infile ...

DESCRIPTION

       AMIDE  is a program intended for viewing and analyzing 3D medical imaging data sets.  In addition to the program's own internal format (XML
       Image Format=XIF), the program can read in a variety of standard medical file formats using the MedCon medical imaging conversion  library.
       For  a  list  of  the  file formats that MedCon supports, please see its manual page.  For additional information on AMIDE, please view the
       AMIDE help documentation, or go to the AMIDE web page: <http://amide.sourceforge.net>.

SEE ALSO

       gpl(7), medcon(1), medcon(1)

BUGS

       Bugs can be reported to the amide user's list (amide-users@lists.sourceforge.net).

AUTHOR

       AMIDE was written by Andreas Loening. For a list of additional contributors, please see the AUTHORS file.

amide-0.8.21							    2007-07-12								  AMIDE(1)

M-ANLZ(4)						     Kernel Interfaces Manual							 M-ANLZ(4)

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).

  e-mail:   enlf-at-users.sourceforge.net   www:   http://xmedcon.sourceforge.net

																	 M-ANLZ(4)