VBANVisionX V4
NAME
vban − nodule blob analysis
SYNOPSISvban [-H] [if=<inputfile>] [x=<value>] [y=<value>] [z=<value>] [r=<value>] [nod=<value>] [th=<value>] [ps=<value>] [tf=<value>] [tr=<value>] [af=<value>] [ar=<value>] [vb=<value>] [dr=<value>] [rs=<value>] [-a] [-A] [-b] [-c] [-s] [-v] [-d] [-f] [-rm] [-i] [-wi] [-F] [-p] [p=<value>] [tl=<value>] [-G] [reg=<value>] [-hm] [-]
DESCRIPTIONvban extracts a nodule from a high-resolution CT image, segments the nodule, generates vpna-style nodule images, and creates 3d and colorized visualizations of the nodule. The algorithm requires a point (x,y,z) inside the nodule. If no point is given, then the algorithm will use the seed stored in the nod.en file for the selected nodule. The seed is required for the analysis of a new nodule.
Alternatively, two points can be used to specify the center of the nodule and the edge of the non-solid region of the nodule.
VBAN also does non-solid analysis, using a low threshold and a simple morphological filter to extract the non-solid region.
When reanalyzing a nodule, VBAN will use all the previous segmentation options (stored in nod.en file) unless explicitly changed on the command line.
By default a window operation is perfomed to remove the imapact of any bone regions at -24 HU. If the -bf option is specified this windowing is not performed.
NOTE: The meaning of threshold values was changed to HU instead of pixel values in version 3.13.
OPTIONS|
if= |
The input image: a CT DICOM image, preferably high-resolution. | ||
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x= |
The nodule location in x (required the first time). | ||
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y= |
The nodule location in y (required the first time). | ||
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z= |
The nodule location in z (required the first time). | ||
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r= |
Initial guess of the radius of the nodule (default=1) | ||
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nod= |
The nodule number (default creates a new nodule). | ||
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ps= |
The pleural segmentation method (f=surface fitting, c=clipping plane). The default method is surface fitting (if vban 3.10 or later was used previously). | ||
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th= |
HU threshold for segmenting the nodule (default=-400 HU) | ||
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tf= |
Parameter for finding the nodule (default=-674HU for pleural, -574 for normal) | ||
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tr= |
Parameter for clipping a nodule from the wall (default=45) | ||
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af= |
Adjust sizing parameter: (-2=even smaller, -1=smaller, 0=nochange, 1=larger, 2=even larger). This is cumulative and the final adjustment is stored in nod.en as n?af. | ||
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ar= |
Adjust pleural segmentation parameter: (-2=even less, -1=less, 0=nochange, 1=more, 2=even more). This is cumulative and the final adjustment is stored in nod.en as n?ar. | ||
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vb= |
Force a kernel size for vbfilt (vessel removal). | ||
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dr= |
Force an intial direction for vrmwall (pleural surface clipping plane) | ||
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rs= |
x,y,z: use a custom resampled nodule seed point. useful when the nodule is very irregular and the resampled seed point is not in the nodule anymore. | ||
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-a |
threshold using an adaptive threshold that is the midpoint between soft tissue and parenchyma peaks of the histogram of the anistropic data. | ||
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-A |
threshold using the -a threshold for nodules less than 5 mm in size. | ||
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-b |
threshold using adaptive threshold on resampled isotropic data. | ||
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-c |
nothing - for compatability with old versions | ||
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-s |
skip analysis and save coordinates to nod.en. The nodule can be analyzed later using vban nod=<nodule number> | ||
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-v |
Verbose option | ||
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-d |
Show each command of the extraction and segmentation algorithm. | ||
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-f |
Don’t remove all the temporary files. For debugging purposes. | ||
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-rm |
Remove all nodule files in the directory except for nod.en | ||
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-i |
Output the nodule number, nodule type, volume, and surface area in shell format. | ||
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-wi |
The same as -i except in wish format. | ||
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-F |
Feedback verbose: output the algorithm’s progress for vnodule. | ||
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-p |
output simple profiling information. | ||
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p= |
x1,y1,z1,[x2,y2,z2] -- two-point method. The first point is in the center of the solid-component of the nodule. The optional second point is on the extent of the non-solid component of the nodule, and indicates a sub-solid nodule. | ||
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tl= |
HU threshold for non-solid component (default=-768HU) | ||
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-G |
Do not do non-solid analysis (compatible with vban version 1) | ||
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reg= |
register the current nodule to this nodule before segmentation | ||
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-hm |
perform histogram matching after registration | ||
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-bf |
Do not do bone windowing (at -24 HU). |
VBAN outputs several files regarding the nodule segmentation. All the nodule segmentation parameters are stored in the nod.en file. The nodule images have are prefixed with an "n" and the nodule number. Here is a list of output files for the various analysis options:
STANDARD SOLID
NODULE ANALYSIS
nod.en - nodule info file
n1.vc - colorized nodule
n1.vf - nodule (float)
n1.vx - nodule (byte)
n1r.vc - colorized resampled nodule
n1r.vf - resampled nodule (float), possibly registered
n1r.vx - resampled nodule (byte), possibly registered
n1t.vd - nodule 3d model
n1t.vx - segmented solid component
n1th.vx - thresholded nodule (high threshold)
NON-SOLID
ANALYSIS
n1tl.vx - thresholded nodule (low threshold)
n1ns.vx - segmented non-solid componenet
ADAPTIVE
THRESHOLD OPTION (-a or -A)
n1.hist - combined histogram of parenchyma and solid tissue
n1.hist1 - histogram of parenchyma peak
n1.hist2 - histogram of solid tissue peak
REGISTRATION
OPTION
n2g.vf - difference image between registered images
n2m.vs - registered image montage
n2o.vf - the original resampled image before
registration
SEGMENTATION
ADJUSTMENT OPTION
n2g.vx - segmentation adustment image showing growth,
atropy, and missegmentation of the nodule.
nod.en is a list of key=value pairs. The parameters are listed below.
GLOBAL
PARAMETERS
cname - case name
nnod - number of nodules in the file
vbanth - high threshold (in HU, for solid analysis)
vbantl - low threshold (in HU, for analysis)
vox - isotropic voxel resolution (in mm)
th - threshold (not used by current vban versions, for vpna)
mseg - (not used by current vban versions, for vpna)
NODULE-SPECIFIC
PARAMETERS
These all have the nodule number prepended to the name, for
example, n1xyres
cs - resampled ROI size
os - ROI size
ps - pleural surface fitting method
reg - nodule registed to (0 for no registration)
rggorr - resampled ggo radius
rguess - radius guess (r= parameter)
rnodl - resampled nodule location
rseed - resampled seed point location
seed - seed point
sslc - not used by current vban versions, indicates the
first slice
surf - area of surface
surfns - area of non-solid surface
vban - vban version used for nodule analysis
vol - volume of solid
volns - volume of non-solid
xh - x-hi of bounding box
xl - x-lo of bounding box
xyres - xy resolution
yh - y-hi of bounding box
yl - y-lo of bounding box
zres - z resolution
Only works on DICOM images.
BUGS--
SEE ALSOv3roi(1), vfindnod(1), vbfilt(1), vrmwall(1), vcolornod(1), vssfilt(1), v3regrb(1), vathresh(1), vhistm(1), vsfit(1)
AUTHORA. B. Chan, Fall 2001