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cmtk-vol2csv - Online in the Cloud

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PROGRAM:

NAME


vol2csv - Compute regional volumes and write to CSV file.

SYNOPSIS


vol2csv RegionsImage DensityImages

DESCRIPTION


This tool computes the volumes of regions in a label image. It optionally accepts density
maps (e.g., for different tissues) and computes and prints the per-region content for
each. Also, the tool can accept an optional 'pixel volume' map to account for local pixel
volume variations, e.g., due to spatial distortion.

OPTIONS


Global Toolkit Options (these are shared by all CMTK tools)
--help
Write list of basic command line options to standard output.

--help-all
Write complete list of basic and advanced command line options to standard output.

--wiki
Write list of command line options to standard output in MediaWiki markup.

--man
Write man page source in 'nroff' markup to standard output.

--version
Write toolkit version to standard output.

--echo
Write the current command line to standard output.

--verbose-level <integer>
Set verbosity level.

--verbose, -v
Increment verbosity level by 1 (deprecated; supported for backward compatibility).

--threads <integer>
Set maximum number of parallel threads (for POSIX threads and OpenMP).

Input Options
--normalize-densities <double>
Optional normalization factor for density images. Typically, the values in the
density images should be in the range 0..1, but often such images are scaled to
different ranges to accomodate storage as integers. If, for example, densities are
stored as values 0..255, set this paramater to 255. [Default: 1]

--labels-file <string>
If provided, this text file contains names for all labels in the regions image. These
names are then used to label the rows of the CSV output. [Default: NONE]

Correction Options
--pixel-scale-factor <double>
If provided, this global scale factor is applied to all pixel volumes to compensate
for deviations between world and image scale. [Default: 1]

--pixel-scale-image <image-path>
If provided, this volume contains scale factors for the volume of each pixel. This is
typically the Jacobian determinant map of a spatial unwarping deformation. [Default:
NONE]

Output Options
--density-labels <string>
This option can be used to provide labels for the density maps, which are used as
column labels in the output. Labels must be separated by commas and must not contain
any unescaped spaces. [Default: NONE]

--output <string>, -o <string>
If provided, program output is written to this file. If not provided, output is
written to the STDOUT stream. [Default: NONE]

AUTHORS


Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R.
Maurer, Daniel B. Russakoff, and Yaroslav Halchenko

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