VCHEST | VisionX V4 |
vchest − Add, extract, or delete a segmented organ from an organ map
SYNOPSISvchest [-H] [if=<inputfile>] [ig=<inputfile>] [of=<outputprefix>] [o=] [-a] [-o] [-e] [-d] [-c] [-l] [-t] [-v]
DESCRIPTIONVchest is a VisionX program used to store and organize templates of segmented organs from whole lung CT scans. It is used in conjunction with various programs that segment organs and structures in the body. First a region is segmented, such as the lungs, ribs, or heart. In order to extract this region from the rest of the image, a binary mask representing the same shape of the organ is used. Performing a logical AND operation between the mask and the image will produce only the region of interest and eliminate the background regions.
Vchest creates a 3D image structure comprised of many of these masks- one for each segmented structure. Each organ has a corresponding number code to allow for proper insertion, deletion, and extraction as necessary.
There is a hierarchy of organs, such that specifying one organ will also include all its subcomponents. For example, the lung may consist of both the left and right lobes. Run with -l to see the hierarchy and all known organ types.
The program may be run with -o flag for the addition of multiple labels. With -o flag, any non-zero values in ig= will be written to the map file.
To create a color map of organs in the chest map, -t flag is used. When -t flag is used ig= should be a chest color configuration file. Refer to v3view’s man page for details on the color file.
OPTIONS|
if= |
Input Image map | ||
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ig= |
Input Image: segmented organ (add only) | ||
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of= |
Output File (new map if adding, organ mask if extracting) | ||
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o= |
organ to extract/add (use -l flag to see listing) | ||
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-a |
Add an organ mask to the map | ||
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-a |
Write any non-zero voxel in ig= to the map | ||
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-e |
Extract an organ mask from the map | ||
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-d |
Permanently delete an organ from the map | ||
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-c |
Check to see if an organ exists in the map | ||
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-l |
List all known organ types in their hierarchy | ||
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-t |
Output true color organ map | ||
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-v |
Verbose mode |
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* |
Handles only byte images |
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SEE ALSO--
vlan, vslung
Jaesung Lee, Benjamin Stein, Winter 2002