You may have just upgraded to macOS Catalina 10.15 and noticed that EVERY. SINGLE. TIME. YOU. OPEN. THE. TERMINAL. You get a warning about changing the default shell to zsh instead of bash. There’s an Apple help page about it, but in case you just wanted to google the answer and find it here, the […]
Stop macOS Catalina 10.15 from hounding you about bash
Posted by pete on October 10, 2019
https://blog.cogneurostats.com/2019/10/10/stop-macos-catalina-10-15-from-hounding-you-about-bash/
PsychoPy: Changing background colors selectively
Say that you want to have an experiment where the background color changes based on a particular condition. This is a fairly common thing to do, but it’s necessarily straightforward in PsychoPy. Since every time I write a new experiment, I end up googling this and going through the usual steps to try and find […]
Posted by pete on July 10, 2019
https://blog.cogneurostats.com/2019/07/10/psychopy-changing-background-colors-selectively/
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 […]
Posted by pete on April 22, 2019
https://blog.cogneurostats.com/2019/04/22/aligning-partial-volume-fmri-in-afni/
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 […]
Posted by pete on September 5, 2018
https://blog.cogneurostats.com/2018/09/05/rendering-afni-suma-over-the-network/
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 […]
Posted by pete on May 10, 2018
https://blog.cogneurostats.com/2018/05/10/the-better-skullstrip-in-afni/