VEMPH

VisionX V4

NAME

vemph − Calculate the Emphysema Index and generate a 2D coronal projection

SYNOPSIS

vemph [-H] [if=<inputfile>] [of=<outputprefix>] [th=<threshold>] [n=<value>] [-v] [-d] [-a] [-tr] [-x]

DESCRIPTION

vemph calculates the Emphysema Index, which is given as the percentage of the lung whose intensity is below a given threshold [th=] (default threshold -910. The program removes the trachea and creates a 2D coronal projection of the entire scan (scout image). It also color-codes the lung region on a scale ranging from no emphysema to severe emphysema and superimposes it on the scout image. The output files are <outputprefix>map.vx, <outputprefix>emph.vx and <outputprefix>proj.vx. Note that <outputprefix> itself is not created. In general, vlan
shoud be used as the interface to vemph.

vemph will generate a coronal projection for full lung scans and return an axial projection for focused scans. The -a flag will force an axial projection.

ALGORITHM

First the lung is segmented (if it is not already done so) using vslung in the same manner as in .I vlan, generating <outputprefix>map.vx. If <outputprefix>map.vx is already present, the segmentation is skipped. The airway is then removed through vsairw, unless supressed by the -tr flag. The final segmented lung parenchyma is further segmented into emphysematous regions. The threshold for determining emphysema is defaulted at -910 HU below which all pixels are considered air. The threshold can be varied using [th=]. Emphysema Index is the ratio of air pixels to total lung pixels times 100.

The scout image (2D coronal projection) is generated using v3mip and averaging all the pixels onto a single plane. To generate the color-coded lung image, the image is broken into segments coronally. The worst-case emphysema index of a given segment is chosen as the representative value for that row. These values are then color coded and superimposed on the scout image.

vemph will detect whether the scan is of a full lung or of a focused region. This is done by calculating the height of the scan and assessing whether it is a full lung or not.

OPTIONS

	if=		Input File -- a 3D CT scan, either whole lung or focused
	of=		Output file prefix -- The output images are <outfile>lung.vx (segmented lung), <outfile>proj.vx (2D projection), and <outfile>emph.vx (color coded image).
	th=		Threshold -- Threshold for determining emphysema index entered in H.U. Generally used thresholds fall between -910 and -950. Default=-910
	n=		Number of Segments -- Divide the lung into n segments to choose the worst case Emphysema Index. Default=16 for coronal projections and 4 for axial projections.
	-tr		Supress tracheal extraction
	-a		Force axial projection
	-x		Expidited segementation
	-v		Verbose operation: output each command as it is processed.
	-d		Debug operation: do not delete intermediate files for debugging

CONSTRAINTS

	*		Can only handle short images
	*		Requires vslung. Requires vsairw (unless -tr flag specified).
	*		In general, use vlan as the interface to vemph.

BUGS

SEE ALSO

--
vlan, vslung, vstra

AUTHOR

Benjamin Stein, Fall 2001 Brad Keller, Spring 2007