All posts for the month May, 2013

Single Subject Analysis in AFNI

AFNI has three major avenues to running a single subject analysis.  1) You can use to configure the analysis in a Graphical User Interface (GUI); 2) You can use to specify the analysis using the command line; 3) You can write your own command line commands in your own script, which calls each […]

Basics of DTI Analysis (FSL)

FSL has a complete pipeline for converting Diffusion Weighted Images (DWI) to Diffusion Tensor Images (DTI) using one of two pipelines: 1) “Tract-Based Spatial Statistics” or 2) Probabilistic Tractography (via Bedpostx and probtrackx).  The graphic below shows a rough overview of each.   The analysis with FSL is fairly straight forward.  If you wish, you can […]

Quality Checking fMRI

You can never be too careful in terms of data quality.  AFNI offers a number of checks on the data via the automated @ss_review_basic and @ss_review_driver generated by  But occasionally you need more information!  And also if you’re comparing data across multiple scanners, it’s not a bad idea to have some of these numbers […]

Source Code Available

Some time ago, I made available a series of custom-built software packages for helping perform EEG/ERP Analysis.  I have now finished uploading the source code to my github repository.  All of the programs were written in Objective-C, many of them fairly early in my programming career (forgive the comments or lack of comments!).  If you […]