intensity_statistics

compute intensity statistics within labelled regions of a volume

intensity_statistics volume.mnc input.tag|input.mnc|none [dump_file|none] [median]

DESCRIPTION

intensity_statistics computes statistics (mean, standard deviation, min, max, and optionally the median) for the voxel intensities in a MINC volume. If an input tag file or label volume is specified, only voxels within the defined region of interest are considered. If none is given as the input, all voxels are included. If a dump file is specified, all individual intensity values are written to that file. If median is specified as the last argument, the median is also computed and reported.

OPTIONS

This tool uses positional arguments only. There are no named options.

volume.mnc

The input MINC volume.

input.tag|input.mnc|none

A tag file or label volume defining the region of interest, or none for the whole volume.

dump_file|none

An output file for dumping all intensity values, or none to skip.

median

Optional keyword to also compute the median.

EXAMPLES

Compute statistics for the entire volume:

intensity_statistics volume.mnc none

Compute statistics within a labelled region including the median:

intensity_statistics volume.mnc labels.mnc none median

Dump all intensity values from a tag-defined region:

intensity_statistics volume.mnc region.tag intensities.txt

AUTHOR

David MacDonald - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.

COPYRIGHTS

Copyright © by David MacDonald

SEE ALSO

mincstats histogram_volume get_tic