Department of Psychiatry
Penn Behavioral Health

Neuropsychiatry Section

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Other Software

The Brain Behavior Laboratory makes some of its software available to other researchers in order to promote the advancement of brain research and to facilitate replication of results obtained here.

This software is provided under an Open Source (tm) license, which permits free use, modification, and redistribution provided that proper credit is given; the complete license terms can be read here.

The use of an Open Source license is an experiment on our part; we have the following reasons for believing that the experiment is worthwhile: First, we believe that software is a form of scientific knowledge and that science advances most rapidly when we can build on each other's work rather than re-implementing each other's wheels. We hope that the people who find our software useful will reciprocate by contributing bug fixes and other improvements to be folded back into our master copy for future releases. Second, we find that we write better software when we expect that dozens of people will be reading our code than when we are writing just for ourselves. Finally, we would rather spend our time doing science rather than trying to monitor and enforce a more restrictive license.

These packages are currently maintained by Paul Hughett at hughett@bbl.med.upenn.edu, who will be happy to receive bug reports, and even happier to receive bug fixes or other improvements. The NRIA and segm packages are considered obsolete and are no longer being actively maintained; BBLimage will eventually include more flexible replacements for these programs.

 

PyVox

BBL's flagship product is PyVox (formerly known as BBLimage), a collection of image processing tools for registering MR images, extracting the brain volume, and segmenting it into CSF and gray and white matter. See PyVox home page for more details.

 

loc - Multi-lingual code counter

The loc program counts lines of code in multiple source files and directories, with heuristic rules to determine the language in which each source file is written. The program currently supports C, C++, Perl, Python, and scripts.

loc-1.0.1.src.tgz (2001/09/05, 8 KB)

 

Segm - Segmentation of MR images of the brain

The segm package includes the adaptive K-means segmentation algorithms developed by Michelle Yan. These have been very useful at BBL for our specific imaging protocols but have not proven adaptable to other protocols.

segm-0.90.src.tgz (2000/10/06, 600 KB)

 

NRIA - New Region of Interest Analysis

NRIA is an XView-based interactive image analysis program developed and used at BBL and which runs under Solaris 2.5 through 2.7. Unfortunately, it is unsupported, undocumented, and not recommended except to those few people who have learned how to use it while in residence at BBL. We include it here primarily for former BBL students who have taken it with them and want to have the latest version.

nria-1.0.6.src.tgz (1999/07/07, 1.3 MB)