AFNI (Analysis of Functional NeuroImages) includes SUMA (Surface Mapping with AFNI) for displaying brains in 3D. AFNI already includes a 3D Render plugin (shown below), capable for displaying fMRI results in 3D. But SUMA offers a few additional benefits, not the least of which is the ability to click and rotate the image by hand […]
Displaying fMRI results on Surfaces with SUMA
Posted by pete on September 26, 2013
https://blog.cogneurostats.com/2013/09/26/displaying-fmri-results-on-surfaces-with-suma/
Connectivity Analysis in AFNI (Part 1)
I’ve written before about how AFNI offers users the ability to perform the same or very similar analyses using a variety of tools. Performing connectivity analysis is no different. First of all, most people who are talking about connectivity are really referring to “seed connectivity” (sometimes called functional connectivity or fcMRI), whereby one region of […]
Posted by pete on September 17, 2013
https://blog.cogneurostats.com/2013/09/17/connectivity-analysis-in-afni-part-1/
Finding ERP Noise Outliers
There are plenty of points in ERP data analysis that can be subjective. But that doesn’t mean that they have to be! One subjective point is determining the noise level of your subjects. If you’re using Net Station (EGI), you can check an option in the “Averaging” Waveform tool to calculate noise estimates. This will […]
Posted by pete on September 9, 2013
https://blog.cogneurostats.com/2013/09/09/finding-erp-noise-outliers/
Rotating bvecs for DTI fitting
Update: While these methods continue to be useful, I now recommend using TORTOISE for preprocessing DTI. The TORTOISE pipeline includes methods for (among other things) reducing distortions from EPI artifacts, eddy current correction, correcting for motion, rotating b-vecs, and co-registration to an anatomical image. There are instructions for using the newest version here. Most […]
Posted by pete on September 6, 2013
https://blog.cogneurostats.com/2013/09/06/rotating-bvecs-for-dti-fitting/
Creating AFNI images via command line and Xvfb
Quite a while ago, I wrote a post about making automated snapshots of MRI activation with AFNI. One of the things I always appreciated about FSL was that they provided a series of ready-made images to show off where activation was in the brain for a given analysis (at least using FEAT). So when I […]
Posted by pete on September 3, 2013
https://blog.cogneurostats.com/2013/09/03/generating-activation-maps-in-afni-without-opening-x11/