University of Debrecen, Medical and Health Science Centre

 Department of Nuclear Medicine

Nagyerdei krt. 98, Debrecen, Hungary. Phone/fax: +36 52 255-500

PROPOSAL:

MINC extension to handle basic data types of Nuclear Medicine

József  Varga, Univ. of Debrecen, 08/13/2002

•  Aim
•  Principle
•  Implementation
•  Examples

Aim:

Although the documentation of the MINC package claims that "it provides a standard for dimension, variable and attribute names suitable for medical imaging", in fact its use has been restricted to reconstructed tomographic data sets, as MINC versions up to 1.0 handle only four dimension variables: xspace, yspace, zspace and time.

The aim of the present extension is to provide and handle additional dimension variables so that the MINC package be able to describe all the image sets regularly used in nuclear medicine, including static, dynamic and gated planar, (SPECT and PET) acquired tomographic, and gated tomographic studies.

The modifications and additions described below were added to and tested under the Windows version of the MINC package; however, they should work on UNIX platforms as well.

Principle:

Dimension variables:

Dimensions of different study types:

The slowest changing dimension is written first.

Limitations:

• Multiple detectors are not implemented yet
• Time sequence of gated studies is not implemented
• Overlapping views (acquisition for wholebody imaging) are not handled.

In all these cases multiple MINC files can be used.

Implementation:

• As in gated studies the "gate" dimension is in time units, only an additional attribute (MIrecurrence) is used to label the "noncyclic" (default) or "cyclic" nature of the time dimension.
• "Projection" and "bin" are handled the same way as regular spatial dimensions x,y,z, except that direction cosines are not applicable in this case.
• "Energy", "view" and "compartment" variables are string arrays, implemented as 2D character blocks.
• "Time" and "time-width" variables can be present even if time is not a dimension of the image variable.
  In this case they represent the start time(s) and duration(s) of the images, respectively.
• The content of the "time" variable can be either relative to the start time of the first acquisition in a series (when "time" is a dimension),
  or the time (in seconds) elapsed from Jan. 1, 1970 (e.g. for static planar and tomo).
• We kept the principle of "one file - one image variable" so as not to deviate too much from the original MINC package.
  As a result, only images of the same matrix size can be stored in a single MINC file.
• In all cases when the data cannot be handled even with the extended dimensions, the use of several MINC files is suggested.

New source files:

• minc_varlists_ext.h
  (instead of minc_varlists.h)
• minc_convenience_ext.c

Modifications:

minc_convenience.c:

• #include <minc_varlists_ext.h> // instead of minc_varlists.h
• "private" label of MI_is_in_list() has been removed

minc.h:

• #include <float.h>
• #define MI_EXTVAR "Extended MINC variable"
• #define MI_EXT_VERSION "MINC Version 1.01"
   
• /* MINC extension: Dimension names and names of associated variables */
  
  #define MIprojection "projection"
  #define MIpfrequency "pfrequency"
  #define MIbin "bin"
  #define MIbfrequency "bfrequency"
  #define MIview "view"
  #define MIenergy "energy"
  #define MIcompartment "compartment"
  
  #define MIprojection_width "projection_width"
  #define MIpfrequency_width "pfrequency_width"
  #define MIbin_width "projection_width"
  #define MIbfrequency_width "pfrequency_width"
   
• /* For dimensions in the MINC extension */
  #define MIrecurrence "recurrence"
• /* MIrecurrence */
  #define MI_NONCYCLIC "noncyclic" // default
  #define MI_CYCLIC "cyclic___"
   
• /* Units */
  #define MI_sec "sec"
   
• /* Extensions to handle basic NM study types */
  public int micreate_string_variable(int cdfid, char *name, int maxlen, int dimid );
  public int miwrite_string_variable( int cdfid, int tx_id, int recnum, char *tx_val );
  public int miread_string_variable( int cdfid, int tx_id, int recnum, char *tx_val, int maxlen );
  #define DEF_STEP DBL_MAX
  #define DEF_START DBL_MAX
  #define MAXLABELLENGTH 33
  public int micreate_ext_dim_variable (int cdfid, char *name, nc_type datatype, int dimlength, int irreg, char *unit, int *varidp, double dimstep, double dimstart );

Examples:

These examples were listed using the (modified) "ncdump.exe", included in the binary package.

• Static planar
• Dynamic planar
• Gated planar
• Acquired SPECT
• Reconstructed SPECT

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Last changed: 2011.04.12.