This page contains an annotated list of software program files written at the Waisman Brain Imaging Lab for analyzing fMRI data. Many of these programs were written to compare software tools (AFNI, AIR, FSL, SPM, VoxBo) using human and phantom data.

A variety of languages were used, including Matlab, IDL, C, Perl, and Python. In general, each language had a specific use:

The directory names in this document assume an unspecified top-level directory. When the programs were created, the top-level directory was:
The unspecified directory should facilitate copying the programs to other locations while maintaining the same organization of the subdirectories.

If you would like to download any of these software programs, please email Terry Oakes at: troakes - at - wisc - dot - edu



Text-files with alternative descriptions which may augment what you see on this page.

Analysis programs

The programs are categorized by language (C, matlab, IDL, Perl, Python).

C programs

The few C programs are for using AIR.

IDL programs

Mostly for phantom creation and analysis. See the file, ".../idl/kw_scripts/kw_script_description.txt" for additional details.

Perl programs

During the course of this work we moved from using Perl to Python for most of our scripting needs. Few of the Perl scripts were migrated to Python. The (older) Perl programs worked fine when we last used them, but we haven't checked them since, or updated them at all.

Python (higher-level scripts for calling other analysis programs):

AIR wrappers

FSL wrappers

fMRI tools-specific programs:

Utilities for image processing

Coregistration scripts

Python Library collections: