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Scan2MCNP


Segmented IMG Files


In a segmented file, the pixel values correspond to identified objects, such as organs, rather than image intensities. Before loading such a file, Segmented should be checked on the IMG Parameters dialog (or the corresponding entry present in the .imd file).

Zubal Data Slice
A frame from one of the Zubal data sets (noodle.med.yale.edu/zubal/).

A Segmentation Data file (read from the Read submenu of the File menu) maps the pixel values to MCNP materials and cells and specifies the colors with which Scan2MCNP displays the data. There is one line per pixel value containing the value, cell, material, name, and color. All 5 entries must be present on each line. The following is a portion of one file:
0   200 2   outside_phantom black
9   -1  10  skeletal_muscle Lightred
10  -1  12  lungs   blue
11  -1  10  heart   orange
12  -1  10  liver   brown
13  -1  10  gall_bladder    yellow
14  -1  10  kidney  brown
15  -1  10  pharynx #AA0B4D
16  -1  10  esophagus 150
17  -1  10  stomach violet
MCNP input cannot be generated if an entry is missing for a pixel value in the data (even if pixel with that value are not converted due to cropping or frame limits). The data may or may not be accompanied by a segmentation file in the correct format.

The MCNP geometry should be a lattice (rather than cells). A universe containing a single cell is created for each cell specified in the segmentation data. The universe and cells numbers are the same. The cell entry can be a positive cell number or -1. The negative value is a quick way to specify a cell number with the same value as the pixel value (in the example, the lungs are represented by universe and cell 10). A positive cell number must be specified for non positive values (such as the first line). Multiple values can be mapped to the same cell. For example, different identified structures in the brain can be mapped to a single brain cell.
The third entry is the material number in the material library. The name cannot contain spaces (these are used a delimiters when parsing the file). The name appears in the status bar in the pixel query mode and as a comment in the MCNP cell definition.

The color is specified in one of three ways. It can be one of 16 names:

White    Red    Green    Purple    Blue    Magenta    Yellow    Black Brown    Orange    Pink    Lightred    Gray    DarkGray    DrkGreen    Violet
or enough letters to permit an unambiguous choice from these names:
W R GRE    PU BLU M Y BLA BR O PI L GRA DA DR V
Explicit red, green, and blue components can be given as
#RRGGBB
where each of RR, GG, and BB are numbers in hexadecimal between 0 (00) and 255 (FF). Values less than F must be padded on the left with 0, such as 0F. The leading # sign is mandatory. An integer between 0 and 255 means that the color is the color of that intensity using the current color scheme.

The MCNP conversion must use a single pixel per voxel cell. Material mixing is not supported for segmented data.



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