Aligning Partial Volume fMRI in AFNI

One of the benefits of high-resolution fMRI (e.g. 7T+) is the ability to see smaller structures and even discern layers of the human cortex (examples: motor cortex and DLPFC). One of the frustrating things about doing sub-1mm resolution is that you’re often constrained to partial volume coverage. Which means that you generally have something that […]

Rendering AFNI/SUMA Over the Network

This is mostly a quick note to remind myself how to do this, since I spent about 30 minutes today “remembering” (synonymous with googling) how I got this to work last time! That said: Once upon a time, many of us would connect to a remote (usually linux) server and run graphical programs over the […]

The better skullstrip in AFNI

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 […]

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 […]

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 […]