VNCGEN | VisionX V4 |
vncgen − generate nodule candidates from a whole lung CT scan.
SYNOPSISvncgen [if=] [of=] [k=] [xy=] [z=] [p=] [po=] [i=] [x=] [-u] [s=] [p=] [po=] [mz=] [oz] [th=] [sx=] [sz=] [-sh] [-b] [-m] [-d] [-v] [-c] [-g]
DESCRIPTIONvncgen program generates nodule candidates from a whole lung CT scan.
A multi-region spherical filter is used to generate nodule candidate regions. The filter has inner, middle and outer regions. The inner region detects the portion of the nodule characterized by the minimum inscribed sphere (region of inclusion). This region is circumscribed by the middle region which accommodates the nodule’s irregularities introduced due to spiculations and partial-volume voxels effect. The outer region detects the nodule candidate’s low intensity surrounding region(region of exclusion). To detect nodules of different sizes, a sequence of filters with increasing size( mininum size specified by [i=] and maximum size specified by [x=]) are used with filter step size specified by [s=], [mz=] and [oz=] for inner, middle and outer shell respctively. Every pixel location is tested if its inner volume occupancy is greater than [p=] and its outer volume occupancy is less than [po=] for a particular filter before the filter size is incremented.
The input image in-plane and axial resolutions are automatically read from the image header file. These values can also be set directly by using [xy=] and [z=] options. Border pixels can be ignored from nodule candidates consideration using the [-b] option. The program outputs potential nodule locations in multiple ways. If a text file is specified in k= option, a text file will be generated with a list of potential nodule XYZ coordinates with their associated filter response. In addition, a visionx file with 3D vector element and object ID corresponding to XYZ coordinates of the potential nodule location and object ID respectively can be generated using of= option. A useful visualization tool with potential nodule locations marked with colors overlaid on top of windowed original input image is also available (-c option). The filter response for all pixel locations can be dumped to a text file using [os=] option. Debugging options -v and -d are available to get information about techniques selected and filter response at every pixel location respectively.
OPTIONS|
if= |
input file name for CT scan(accepts short type). | ||
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[of=] |
visionx output file with 3D vector corresponding to XYZ coordinates of nodule location and object ID | ||
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[k=] |
Potential nodules location in text file format | ||
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[os=] |
Filter response info at every pixel location | ||
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[xy=] |
in-plane resolution | ||
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[z=] |
axial direction resolution | ||
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[-u] |
anisotropic data | ||
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[p=] |
inner shell volume percentage threshold | ||
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[po=] |
outer shell volume percentage threshold | ||
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[i=] |
minimum size for the spherical filter | ||
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[x=] |
maximum size for the spherical filter | ||
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[s=] |
step size for the filter | ||
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[mz=] |
step size for the middle shell | ||
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[oz=] |
step size for the outer shell | ||
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[th=] |
image intensity threshold | ||
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[sx=] |
xy scaling factor for the outer most shell | ||
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[sz] |
z scaling factor for the outermost shell | ||
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-sh |
shell script output | ||
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-m |
multi region analysis | ||
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-b |
ignore border pixels | ||
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-v |
selects the verbose mode to print information about intermediate results | ||
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-c |
generate color marked output image for quick visualization (default name IVALdcol.vx) | ||
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-g |
generate files of all filters used for the detection (named filter1.vx, filter2.vx.....) | ||
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-d |
output filter response at every pixel location (useful for debugging) |
Andinet Asmamaw