BIAC fMRI Processing Pipeline

BIAC's Processing Pipeline software consists of two full-featured software systems: one that handles pre-processing of fMRI data as the data is pushed off the scanner and another that handles all subsequent data analysis. Together, these two systems can be used for simplifying complex data analyses.

News

• 2/5/04 - A incomplete performance analysis of the Golgi processing scripts.
• 1/27/04 - There has been some problems with sharity failing on Golgi for some steps. Here is a batch script for those with data on Sharity accessed directories (e.g. Nernst).
• 1/24/04 - Abstract submitted to HBM 2004.

Documentation

• Chuck and Jimmy's Pipeline presentation
• Processing Pipeline Tutorial, How does it all work?
• The abstract we submitted to HBM 2004 provides a general overview.
• Frequently asked questions (FAQ).

Utility Information

• tralign - time slice corrections using SPM99.
• motioncorrect - motion correction using either AIR5.2.5 or SPM99.
• coregister - coregistration using SPM99, allows reslicing option.
• coreg_normalize - coregistration and normalization bundled into one.
• normalize - normalization using SPM99.
• smooth - smoothing using SPM99.
• dircopy - perl script that robustly copies files across filesystems.
• pfile_recon.pl - perl script for epiduke, spiral and invspiral recons.
• checkstatus - utility for checking status of transfer daemon.
• quickhdr.pl - displays header information for dicom files and pfiles.

Related Links

• UNIX tutorial for beginners - simple UNIX tutorial for you Windows users.
• Bash Scripting Guide - Want to do more with your batch scripts? Here is a guide to show you how.
• SPM - suite of Matlab fxns developed by Wellcome implementing Statistical Parametric Mapping.
• AIR 5.2.5- UCLA-developed software that allows automated registration of 2D and 3D images.
• LoadLeveler - IBM's load averaging software for managing serial and parallel jobs.
• LONI Pipeline - UCLA's software for automating complex scientific analyses of data.
• ITK - open-source segmentation and registration toolkit developed to support Human Visible Project.