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

LICENSE

       http://www.fsf.org/licensing/licenses/gpl.html

BUGS

       Report bugs at http://nitrc.org/projects/cmtk/

ACKNOWLEDGMENTS

       CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on
       Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data  Integration  Component.  From
       April  2009  through September 2011, CMTK development and maintenance was supported by the
       NIBIB under Grant EB008381.