m-acr man page

m-acr — ACR/NEMA medical image format (MedCon)

Description

We are absolutely lost in standards, versions and ACR/NEMA dialects. Here you can only read how we handle this format. The format is written in one file with extension `.ima'.

The format consists of a group of fields with different elements, in a serie of tags. Does that explain you something? The image data is stored from left to right and from top to bottom.

The basic defines for the format:

---------------------------------------------------------------------------

#define MDC_ACR_TAG_SIZE 8    /* size of group+element+length */

typedef struct {
  Uint16 group;           /* the kind of group   */
  Uint16 element;         /* the kind of element */
  Uint32  length;         /* the length of data  */
  Uint8   *data;          /* pointer to the data */
} MDC_ACR_TAG;

---------------------------------------------------------------------------

What does the format support or not support:

===========================================================================
Item            Supported                             Not Supported       
===========================================================================
Color Map     : grayscale                                   -
File Endian   : little & big                                -             
Pixeltypes    : all integers (signed/unsigned)        float & double      
===========================================================================
Scaling factors  : quantify & calibrate factors/image  are NOT supported,
                   unless you define your own tags
---------------------------------------------------------------------------
Dimensions/Image : different dimensions for each image are supported
---------------------------------------------------------------------------
Pixeltypes/Image : different pixeltypes for each image are supported
===========================================================================

An ACR/NEMA file could look like this, in fact it is the kind we write:

===========================================================================
GROUP 0x0008 Identifying information
===========================================================================
Uint16  Group   number                : 0x0008
Uint16  Element number                : 0x0000 (first element of any group)
Uint32  Element length  in bytes      : (4)     
Int32   Length of group in bytes      : (X)    (143)
X = [total length of this group] - [total bytes of this first tag (12)] 
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0008
Uint16  Element number                : 0x0001
Uint32  Element length  in bytes      : (4)
Int32   Total bytes to end of file    : Y
Y = [filesize] - [total bytes of first two tags]
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0008
Uint16  Element number                : 0x0010
Uint32  Element length  in bytes      : (12)
char *  Recognition Code              : (ACR-NEMA 2.0)
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0008
Uint16  Element number                : 0x0020
Uint32  Element length  in bytes      : (10)
char *  Study Date                    : yyyy.mm.dd
---------------------------------------------------------------------------
Uint16 Group    number                : 0x0008
Uint16 Element  number                : 0x0030
Uint32 Element length   in bytes      : (14)
char *  Study Time                    : hh.mm.ss.frac_
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0008
Uint16  Element number                : 0x0040
Uint32  Element length  in bytes      : (2)
Int16   Data Set Type                 :   0 = Images
                                        256 = Raw data
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0008
Uint16  Element number                : 0x0060
Uint32  Element length  in bytes      : (2)
char *  Image Modality                : (NM)
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0008
Uint16  Element number                : 0x0070
Uint32  Element length  in bytes      : (24)
char *  Manufacturer                  : (MedCon v?.?? - Erik Nolf)
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0008
Uint16  Element number                : 0x0080
Uint32  Element length  in bytes      : (11)
char *  Institution ID                : (NucMed)
===========================================================================
GROUP 0x0010 Patient Information
===========================================================================
Uint16  Group   number                : 0x0010
Uint16  Element number                : 0x0000
Uint32  Element length  in bytes      : (4)
Int32   Length of group in bytes      : (96)
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0010
Uint16  Element number                : 0x0010
Uint32  Element length  in bytes      : (35)
char *  Patient Name                  :
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0010
Uint16  Element number                : 0x0020
Uint32  Element length  in bytes      : (35)
char *  Patient ID                    : 
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0010
Uint16  Element number                : 0x0040
Uint32  Element length  in bytes      : (2)
char *  Patient Sex                   : M_ = male
                                        F_ = female
                                        O_ = others
===========================================================================
GROUP 0x0018 Acquisition Information
===========================================================================
Uint16  Group   number                : 0x0018
Uint16  Element number                : 0x0000
Uint32  Element length  in bytes      : (4)
Int32   Length of group in bytes      : (122)
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0018
Uint16  Element number                : 0x0030
Uint32  Element length  in bytes      : 32
char *  Radionuclide                  : 
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0018
Uint16  Element number                : 0x0050
Uint32  Element length  in bytes      : (13)
char *  Slice Thickness in mm         : (+0.000000e+00)
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0018
Uint16  Element number                : 0x0088
Uint32  Element length  in bytes      : (13)
char *  Slice Spacing   in mm         : (+0.000000e+00)
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0018
Uint16  Element number                : 0x1120
Uint32  Element length  in bytes      : (13)
float   Gantry Tilt     in degrees    : (+0.000000e+00)
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0018
Uint16  Element number                : 0x1160
Uint32  Element length  in bytes      : (32)
char *  Filter Type                   :
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0018
Uint16  Element number                : 0x5100
Uint32  Element length  in bytes      : (32)
char *  Patient Position              : (supine)
                                        supine = face-up     on    the table
                                        prone  = face-down towards the table
                                        other?
===========================================================================
GROUP 0x0020 Relationship Information
===========================================================================
Uint16  Group   number                : 0x0020
Uint16  Element number                : 0x0000
Uint32  Element length  in bytes      : (4)
Int32   Length of group in bytes      : (352)
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0020
Uint16  Element number                : 0x0010
Uint32  Element length  in bytes      : (10)
char *  Study ID                      :
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0020
Uint16  Element number                : 0x0013
Uint32  Element length  in bytes      : (6)
char *  Image Number                  :
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0020
Uint16  Element number                : 0x0020
Uint32  Element length  in bytes      : (32)
char *  Patient Orientation           : (L\P)

 (direction of image row in patient\direction of image column in patient)

   'L' = Left  (hand)   'A' = Anterior  (to front)   'H' = Head
   'R' = Right (hand)   'P' = Posterior (to back)    'F' = Feet

---------------------------------------------------------------------------
Uint16  Group   number                : 0x0020
Uint16  Element number                : 0x0030
Uint32  Element length  in bytes      : (41)
char *  Image Position  in mm         : 

                        * * * * * * * * * * * * *
Gives the 3D equipment based coordinates of the upper left hand corner
in the image. Example: (+0.000000e+00\+0.000000e+00\+0.000000e+00)
                         =X-axis         =Y-axis       =Z-axis
"When facing the front of the gantry (equipment device), and with the 
 gantry in a neutral (untilted) position, the x-axis is increasing to the
 right; the y-axis is increasing down (gravitational attraction); and the
 z-axis is defined as the line orthogonal to x and y, with increasing
 values from the front to the back of the gantry."
 (From a Papyrus 2.3 document: UIN/HCUG 1990, 91)

        
My note: where is its origin? For an ECAT 931 scanner we choose the origin
in the right/back/down point of the gantry
     
      A  
   ______H 
  |\______\F    Looking to the scanner, this is a representation of the 
R |.|.... |  L  volume our scanner detects. My origin is in the point we
   \|_____|     can't see ;-) Our images are transversal slices, beginning
                at the head towards the feet (so patient orientation = L\P)
      P         and the patient position is supine.

Therefore, the coordinates of the first pixel in our images is: 
Image 0:
 -(PIXEL_X_SIZE*PIXELS_IN_X);-(PIXEL_Y_SIZE*PIXELS_IN_Y);-0
Image 1:
 -(PIXEL_X_SIZE*PIXELS_IN_X);-(PIXEL_Y_SIZE*PIXELS_IN_Y);-(SLICE_WIDTH*1)
Image n:
 -(PIXEL_X_SIZE*PIXELS_IN_X);-(PIXEL_Y_SIZE*PIXELS_IN_Y);-(SLICE_WIDTH*N)
                     |                           |
                image width                 image height 

A view of the coordinate system you can see in 0x0020;0x0035.

However, it could all be wrong too! By the way, for DICOM it's retired stuff.
                        * * * * * * * * * * * * *
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0020
Uint16  Element number                : 0x0032
Uint32  Element length  in bytes      : (41)
char *  Image Position (Patient) in mm: 
                        * * * * * * * * * * * * *
The same as above but know based on the coordinate system of the patient.
A DICOM replacement for the above values:
"The direction of the axes is defined fully by the patient's orientation.
The x-axis is increasing to the left hand side of the patient. The y-axis
is increasing to the posterior side of the patient. The z-axis is increasing
toward the head of the patient.

The patient based coordinate system is a right handed system, i.e. the vector
cross product of a unit vector along the positive x-axis and a unit vector 
along the positive y-axis is equal to a unit vector along the positive z-axis.

NOTE: If a patient lies parallel to the ground, face-up on the table, with
      his feet-to-head direction the same as front-to-back direction of the
      imaging equipment, the direction of the axes of the patient based 
      coordinate system and equipment based coordinate system in previous 
      versions of the DICOM Standard will coincide"
(From the NEMA Standards Publication PS3.3(199X)

                        * * * * * * * * * * * * *
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0020
Uint16  Element number                : 0x0032
Uint32  Element length  in bytes      : (83)
char *  Image Orientation             :

                        * * * * * * * * * * * * *
Based on 0x0020;0x0030 these are the direction cosines of a unit vector
on the first row and on the first column based on the equipment coordinate
system (or our patient coordinate system, because they coincide as we 
described above).

                       (to back of the scanner) 
                    +Z (or head of the patient)
                    \
                     \  coordinate system
                      \ 
                       \_ _ _ _ _ _ _ +X (to right of the scanner)
                        |                 (or left  of the patient)
                        |
                        |                                                
                        |
                       +Y (to the ground)
                          (or back of the patient)

                        * * * * * * * * * * * * *

Remember we take transversal slices (Right to Left of patient, Anterior to
Posterior) while the patient is supine with head first in gantry.
Then the images are in the plane XY and the unit vectors are 

   upper left 
   corner of image         (X)
                   + - - - - > (x1,y1,z1 = 1,0,0)
                   |               unit vector on row
                   |
                   |
              (Y)  V (x2,y2,z2 = 0,1,0)
                         unit vector on column

In this case: a) in point (x1,y1,z1)
                   X direction cosinus = +1
                   Y direction cosinus = -0
                   Z direction cosinus = -0
           
              b) in point (x2,y2,z2)
                   X direction cosinus = +0
                   Y direction cosinus = +1
                   Z direction cosinus = +0
 
How about the signs and values? 
                     cos(0 or 360) = +1
                     cos(90)       = +0
                     cos(180)      = -1
                     cos(270)      = -0

The angle between an axis and the vector, you determine with a so called 
"corkscrew-rule": You must turn from THE AXIS towards THE VECTOR (=angle)
the same direction so a corkscrew should proceed in the direction
of an axis orthogonal on the plane formed by THE AXIS and THE VECTOR.
Well, thats what it should be I think. If your images are tilted, it
will be a bit harder, isn't it?

For the above ECAT 931 acquisition an example value should be:

	(+1.000000e+00\-0.000000e+00\+0.000000e+00\
	 +0.000000e+00\+1.000000e+00\-0.000000e+00)

Again, this tag is retired for DICOM ...
                        * * * * * * * * * * * * *
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0020
Uint16  Element number                : 0x0037
Uint32  Element length  in bytes      : (83)
char *  Image Orientation Patient     :

The same as for tag 0x0020;0x0032 but now considered for the patient
coordinate system ...

===========================================================================
GROUP 0x0028 Image Presentation
===========================================================================
Uint16  Group   number                : 0x0028
Uint16  Element number                : 0x0000
Uint32  Element length  in bytes      : (4)
Int32   Length of group in bytes      : (127)
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0028
Uint16  Element number                : 0x0005
Uint32  Element length  in bytes      : (2)
Int16   Image Dimensions              : (2)
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0028
Uint16  Element number                : 0x0010
Uint32  Element length  in bytes      : (2)
Int16   Rows                          :
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0028
Uint16  Element number                : 0x0011
Uint32  Element length  in bytes      : (2)
Int16   Columns                       :
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0028
Uint16  Element number                : 0x0030
Uint32  Element length  in bytes      : (27)
char *  Pixel Size      in mm         : (+0.000000e+00\+0.000000e+00)
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0028
Uint16  Element number                : 0x0060
Uint32  Element length  in bytes      : (4)
char *  Compression code              : (NONE)
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0028
Uint16  Element number                : 0x0100
Uint32  Element length  in bytes      : (2)
Int16   Bits Allocated                : 
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0028
Uint16  Element number                : 0x0101
Uint32  Element length  in bytes      : (2)
Int16   Bits per Pixel                : 
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0028
Uint16  Element number                : 0x0102
Uint32  Element length  in bytes      : (2)
Int16   High Bit                      :
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0028
Uint16  Element number                : 0x0103
Uint32  Element length  in bytes      : (2)
Int16   Pixel Representation          : 0 = unsigned
                                        1 = signed
---------------------------------------------------------------------------
Uint16  Group   number                : 0x0028
Uint16  Element number                : 0x0200
Uint32  Element length  in bytes      : (2)
Int16   Image Location                : (7fe0)
===========================================================================
GROUP 0x7fe0 Pixel Information
===========================================================================
Uint16  Group   number                : 0x7fe0
Uint16  Element number                : 0x0000
Uint32  Element length  in bytes      : (4)
Int32   Length of group in bytes      : Z
Z = [imagesize] + 8
---------------------------------------------------------------------------
Uint16  Group   number                : 0x7fe0
Uint16  Element number                : 0x0010
Uint32  Element length  in bytes      : (imagesize)
Uint8 * Image Data                    :             
---------------------------------------------------------------------------

This was an example of an ACR/NEMA file holding one image, as normal ACR/NEMA files do. However, as we are interested in multiple images, we use an ACR/NEMA dialect such as Papyrus. In this case we sequentially concatenate different ACR/NEMA files into one single large file!

Notes

Because of the previous remark, we must notify that in the Element 0x0001 of Group 0x0008, the [filesize] means the filesize in case of this one ACR/NEMA file and NOT the real filesize!

For the Group 0x0028, Element 0x0100: `Bits Allocated'
We only support a multiple of 8.
For the Group 0x0028, Element 0x0102: `High Bit'
We only support `High Bit' = [`Bits per Pixel'] - 1,
so we only accept images stored in the file endian type.

Files

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

See Also

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

m-anlz(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.netwww:http://xmedcon.sourceforge.net

Referenced By

m-anlz(4), m-ecat(4), medcon(1), medcon(3), m-gif(4), m-intf(4), m-inw(4), xmedcon(1), xmedcon-config(1).