For most users of imaging software, we use the skull stripping program included in our distribution. If you’re an AFNI user, you probably use 3dSkullStrip, if you use FSL then it’s BET, and of course Freesurfer has their own in recon-step 1. A few years ago, I advocated for using Optibet and even wrote an entirely […]
All posts in category Neuroimaging
The better skullstrip in AFNI
Posted by pete on May 10, 2018
https://blog.cogneurostats.com/2018/05/10/the-better-skullstrip-in-afni/
DTI Statistics with TRACULA data (Part 1)
If you’re reading this post either you’re a loyal fan (yay!) or you’ve run Freesurfer (possibly in parallel) and processed your diffusion data in (hopefully TORTOISE) and then Tracula (also possibly in parallel) and you’re wondering where do you go from here. I’m glad you’re here, that’s probably me talking to myself because I read my own blog […]
Posted by pete on May 22, 2017
https://blog.cogneurostats.com/2017/05/22/statistics-with-tracula-data-part-1/
Preprocessing Diffusion Weighted Images with TORTOISE 3 (Part 1)
A while back, I posted about how to use TORTOISE 2.0/2.5 for preprocessing Diffusion Weighted Images (DWIs), create tensors, and then do blip-up blip-down correction. All of those steps relied on using a graphical user interface (GUI) through a program called IDL to tell TORTOISE what you wanted it to do. This was often a […]
Posted by pete on April 10, 2017
https://blog.cogneurostats.com/2017/04/10/preprocessing-diffusion-weighted-images-with-tortoise-3-part-1/
How to install AFNI on macOS X Sierra
Follow these instructions for Mac OS X 10.11 El Capitain. That’s it! It’s great when stuff continues to just work! Well… mostly. Depending on how you upgraded, you might have to run this command in the terminal to allow you to run applications from unsigned developers: sudo spctl –master-disable But that should really be it.
Posted by pete on November 1, 2016
https://blog.cogneurostats.com/2016/11/01/how-to-install-afni-on-macos-x-sierra/
Performing brain-behavior correlations with 3dttest++
A while ago, I wrote a post for doing brain-behavior correlations with different AFNI programs. And at the time I mentioned that you can do correlations with 3dtest++, but you’d first need to standardize (read: z-score) both the brain and behavior values. The general logic there is that if you’re doing a simple regression (what […]
Posted by pete on October 26, 2016
https://blog.cogneurostats.com/2016/10/26/performing-brain-behavior-correlations-with-3dttest/