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.