Typically when we smooth (aka spatial filter) our fMRI data using a fixed kernel size. And as we know, the size of a smoothing kernel makes some difference in the final results (see below). This shows a group analysis map, the results are more shocking on single subject maps. The common misconception is that you […]
All posts in category MRI
Adjusting MRI Smoothness for Multi-Scanner Comparisons
Posted by pete on October 7, 2013
https://blog.cogneurostats.com/2013/10/07/smoothing-mri-images-in-afni/
Displaying fMRI results on Surfaces with SUMA
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 […]
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/
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/
Writing your own fMRI programs using the AFNI API (Part 1)
I find that it’s fairly rare that I wish there was an AFNI program that did something that cannot be accomplished with existing tools and a bit of creativity. But, if you do find something that requires writing a custom program, the AFNI distribution is both easily accessible and fairly straightforward to code for. Over […]
Posted by pete on August 21, 2013
https://blog.cogneurostats.com/2013/08/21/writing-your-own-fmri-programs-using-the-afni-api-part-1/