voitools

Scripts of inspect volume-of-interest files created by spamalize, and convert them into NIFTI images.

Requires nibabel and, hence, numpy. Should work with python 2.6 and 2.7; 3.0 is not tested yet.

Archived

This is ancient and may not work. Use at your own risk!

Installation

python setup.py install

After some testing, I'll put this up on pypi.

Usage

voi2nii

voi2nii [options] <datafile>

Convert a spamalize .voi file into a set of nifti files.

This program will produce one .nii file per VOI in a VOI group (.voi) file;
the name will be determined by the --pattern parameter.

Usage:
  voi2nii [options] <datafile>
  voi2nii -h | --help

Options:
  --pattern=<pat>       How to name the output. Surround fields in {}.
                        Available fields:
                        base_name   The name of the file the VOI group is
                                    based on
                        cur_name    The current name of the VOI group file
                        voi_number  The index of this VOI
                        voxel_count The number of voxels in the VOI
                        voi_name    The name of this VOI
                        [default: {cur_name}-{voi_name}-{voi_number}.nii]
  --voi-numbers=<nums>  The indexes (starting from 1) of the VOIs to convert.
                        Separate with commas. If not specified, converts all
                        VOIs.
  --out-dir=<dir>       Directory to write the output files [default: .]
  -h --help             Show this screen
  --version             Show version
  -v --verbose          Display debugging information

voi_info

voi_info [options] <datafile>

Print information about a spamalize .voi file.

Usage:
  voi_info [options] <datafile>
  voi_info -h | --help

Options:
  -h --help                 Show this screen
  --version                 Show version
  -v --verbose              Display debugging information

Notes

Spamalize is written in IDL; its arrays are in fortran data order. Orientation and origin information are not included in .voi files; voi2nii writes in RAI orientation with the origin at the center of the volume.

Credits

Spamalize was developed by the most skilled and fantastic Terry Oakes.

voi_tools ships with the excellent docopt and ordereddict libraries.

docopt is copyright © 2013 Vladimir Keleshev, [email protected]

ordereddict is copyright © 2009 Raymond Hettinger