All posts in category MRI

Helpful fMRI QA Tools in AFNI

Apologies for the lack of updates lately!  It’s been… busy. I’ve written in the past about automatically making “snapshots” in AFNI (here) and even doing that without having AFNI taking over you entire screen using Xvfb (here).  These are one way of performing Quality Assurance (QA) on your data, by actually LOOKING at the activation […]

How to Analyze Diffusion Tensor Imaging Data (Review)

After my first year of blogging, I ran a “One Year Review” piece that covered all of the articles that I wrote in that first year.  And that article tends to get hit by search engines fairly often since it was published on December 3, 2013.  Sure, I meant to go back and do a […]

Example use of DTIprep for DWI Quality Checking

In a previous post, we covered using DTIprep for preprocessing of diffusion weighted imaging (DWI) data.  I’ve written a quick script (below) to automate DTIprep for the purposes of running the default QC check.  My workflow has DICOM data automatically downloaded from our PACS server, then automatically converted to NIFTI format, and then organized in the […]

DTIprep for Preprocessing of DWI Data

As I’ve mentioned before, it’s a good idea to do some preprocessing on your diffusion imaging data!  Previous tutorials have covered using AFNI’s built-in tools (Part 1, Part 2, Part 3) as well as the very formidable TORTOISE (Part 1, Part 2, Part 3).  As with most things in NeuroImaging, you have many options when […]

Some exposure to MRI Transforms in AFNI

Transform matrices are confusing!  There, I said it.  If you’ve never taken the time to play around with transform matrices in MRI, I completely understand.  That said, it’s not a bad idea to get some exposure to the world of warping and the matrices that they often depend on.  First of all, there are different […]