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. […]
All posts in category Neuroimaging
Adventures in AFNI ROI combinations
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/
Creating ROIs in AFNI with Coordinates
In the past, I’ve posted on creating ROIs in AFNI and ways to manipulate those ROIs once created. But something that comes up fairly often on the AFNI message boards is how to use 3dcalc to create different ROI shapes. The most common that I’ve found are creating spheres and cubes, I’ve made some crazy […]
Posted by pete on February 5, 2014
https://blog.cogneurostats.com/2014/02/05/advanced-creation-of-rois-in-afni/
TORTOISE Processing of DWI/DTI (Part 2)
Last time, we covered how to use TORTOISE’s DIFF_PREP tool to preprocess Diffusion Weighted Images (DWI) to correct for eddy currents, motion, rotate the b-vectors (alongside the motion correction), and optionally correct b-splines if we used a T2-weighted structural image. The next step is to use DIFF_CALC to fit tensors, inspect the results, measure ROIs, […]
Posted by pete on January 23, 2014
https://blog.cogneurostats.com/2014/01/23/tortoise-processing-of-dwidti-part-2/