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 […]
Basics of DTI Analysis (FSL)
Posted by pete on May 28, 2013
https://blog.cogneurostats.com/2013/05/28/basics-of-dti-analysis-fsl/
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 afni_proc.py. 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 […]
Posted by pete on May 23, 2013
https://blog.cogneurostats.com/2013/05/23/quality-checking-fmri/
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 […]
Posted by pete on May 21, 2013
https://blog.cogneurostats.com/2013/05/21/source-code-available/
Using R with AFNI
AFNI already has a host of programs that use R to analyze MRI data – 3dLME, 3dMVM, 3dMEMA, etc. Suppose you wanted to create your own functions that use R to manipulate data – well here’s a quick introduction. In this quick example, here is how to “Auto Mask” your dataset in R. source(‘path/to/AFNI/AFNIio.R’) thedata […]
Posted by pete on April 9, 2013
https://blog.cogneurostats.com/2013/04/09/using-r-with-afni/
A better way to run AFNI’s uber_subject
I used to use fink, and then I switched to MacPorts; truthfully, neither of them really made me happy. Now I mostly use homebrew, and one real advantage (besides being faster and lighter weight) is that it’s very easy to get AFNI’s GUI programs up and running on a Mac. Install AFNI (you’ve probably already […]
Posted by pete on April 8, 2013
https://blog.cogneurostats.com/2013/04/08/a-better-way-to-run-afnis-uber_subject-p/