vol2csv - Compute regional volumes and write to CSV file.
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
- Write list of basic command line options to standard
- Write complete list of basic and advanced command line
options to standard output.
- Write list of command line options to standard output in
- Write man page source in 'nroff' markup to standard
- Write toolkit version to standard output.
- Write the current command line to standard output.
- --verbose-level <integer>
- Set verbosity level.
- --verbose, -v
- Increment verbosity level by 1 (deprecated; supported for
- --threads <integer>
- Set maximum number of parallel threads (for POSIX threads
- --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]
- --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.
- --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]
- --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.
- --output <string>, -o
- If provided, program output is written to this file. If not
provided, output is written to the STDOUT stream. [Default:
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis,
Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
Report bugs at http://nitrc.org/projects/cmtk/
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