While the information in this post is useful, I recommend users use TORTOISE for processing diffusion data. You can read a tutorial of TORTOISE3 here. I previously described how to do some DTI analyses in AFNI. To review, we could use a linear alignment to the b0 image in order to correct for some eddy […]
All posts in category DTI
Analyzing DTI Data in AFNI (Part 2)
Posted by pete on August 26, 2013
https://blog.cogneurostats.com/2013/08/26/analyzing-dti-data-in-afni-part-2/
Writing your own fMRI programs using the AFNI API (Part 1)
I find that it’s fairly rare that I wish there was an AFNI program that did something that cannot be accomplished with existing tools and a bit of creativity. But, if you do find something that requires writing a custom program, the AFNI distribution is both easily accessible and fairly straightforward to code for. Over […]
Posted by pete on August 21, 2013
https://blog.cogneurostats.com/2013/08/21/writing-your-own-fmri-programs-using-the-afni-api-part-1/
Analyzing DTI Data in AFNI (Part 1)
Previously, I talked about how to process DWI/DTI data in FSL and then visualize the results. AFNI has recently added quite a few tools for analyzing diffusion data. I’ll cover these in the next post, but first I’ll review correction of eddy currents, coregistering the DWI data to the anatomical and fitting tensors. The following […]
Posted by pete on July 18, 2013
https://blog.cogneurostats.com/2013/07/18/analyzing-dti-data-in-afni-part-1/
Visualizing Single Subject DTI Data (FSL)
A few posts ago, I described how to do some basic analyses of Diffusion data. I realize now that I left off the visually cool factor of displaying individual subject data. Once you complete the eddy_correct and dtifit steps in the previous post, several files will be generated for FA (fractional anisotropy), MD (mean diffusivity), […]
Posted by pete on June 6, 2013
https://blog.cogneurostats.com/2013/06/06/visualizing-single-subject-dti-data-fsl/
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 […]
Posted by pete on May 28, 2013
https://blog.cogneurostats.com/2013/05/28/basics-of-dti-analysis-fsl/