It’s been a while since I’ve touched on this topic (Part 1, Part 2). Recently the topic of doing t-tests has come up a lot in the area around where my desk is situated. In vastly over simplified thinking, I think the three most common approaches to using t-tests in MRI data are as follows: […]
Basics of AFNI Group Analyses (Part 3)
Posted by pete on May 5, 2014
https://blog.cogneurostats.com/2014/05/05/basics-of-afni-group-analyses-part-3/
Single Subject Analysis on the Surface (SUMA)
I had previous posted about displaying the fMRI results onto the cortical surface. It’s been brought to my attention that this post wasn’t as clear as it could be! I know, it happens from time to time! So let’s try this again! Let’s start with a straightforward topic – processing data at the single-subejct level on […]
Posted by pete on April 30, 2014
https://blog.cogneurostats.com/2014/04/30/single-subject-analysis-on-the-surface-suma/
Adventures in AFNI ROI combinations
I’ve written about ROI creation in AFNI a few times before (one, two, three). When we draw ROIs or use 3dUndump, we usually end up with multiple ROIs in one file, each with a different label. In contrast, when we use whereami to create atlas regions, we usually end up with one ROI per file. […]
Posted by pete on April 25, 2014
https://blog.cogneurostats.com/2014/04/25/adventures-in-afni-roi-combinations/
R for MRI Lovers (Part 1)
Like many scientists, I learned SPSS a long long time ago. It was free and installed on any computer at my undergraduate institution. And like many people, I found the pull-down menus useful and sometimes endearing. But when I went to grad school I was thrust into a world of using SAS. Many a groans […]
Posted by pete on March 25, 2014
https://blog.cogneurostats.com/2014/03/25/r-for-mri-lovers-part-1/
Dealing with transforms in AFNI (Part 1)
AFNI’s main tool for dealing with transforms is cat_matvec, but in many cases you may not need to use it! Everyone knows that transform matrices are confusing — I’ll do a post later on just covering them — but for now, I think we can all agree that it’s a relief anytime you don’t have to […]
Posted by pete on February 27, 2014
https://blog.cogneurostats.com/2014/02/27/concatenating-transforms-in-afni/