Transform matrices are confusing! There, I said it. If you’ve never taken the time to play around with transform matrices in MRI, I completely understand. That said, it’s not a bad idea to get some exposure to the world of warping and the matrices that they often depend on. First of all, there are different […]
All posts in category MRI
Some exposure to MRI Transforms in AFNI
Posted by pete on January 23, 2015
https://blog.cogneurostats.com/2015/01/23/some-exposure-to-mri-transforms-in-afni/
Intersection Maps in AFNI
I’ve recently been working with a dataset that included the same subjects across two studies (here: study1 and study2) that should give us complimentary information. One of the ways that you can look at data across these two studies is to create “intersection” maps, that show where the brain regions were activated in both studies. Obviously […]
Posted by pete on December 1, 2014
https://blog.cogneurostats.com/2014/12/01/intersection-maps-in-afni/
Tidbits on AFNI’s TENT function
I think we’ve all had that moment where we wonder what exactly our HRF function is doing to give us the results that we see in our data. Using a fixed function regressor can be great for a number of reasons: 1) they don’t require many degrees of freedom, 2) someone else did the hard […]
Posted by pete on October 8, 2014
https://blog.cogneurostats.com/2014/10/08/tidbits-on-afnis-tent-function/
R for MRI Lovers (Part 2)
Writing this post after the first in the series may seem somewhat backwards! Last time we covered reading in data from individual subjects and plotting them as box plots with error bars in R. This time we’ll do something even more straightforward – plotting ROI group effects. If you haven’t already read it, there are […]
Posted by pete on September 3, 2014
https://blog.cogneurostats.com/2014/09/03/r-for-mri-lovers-part-2/
Freesurfer Cortical Thickness Analysis with AFNI/SUMA tools
First let me say that I am a huge huge fan of Freesurfer. It makes my life easier in so many ways by 1) creating surfaces that we can display fMRI results on; 2) giving beautiful cortical and subcortical segmentations for use in the upcoming (soon, really) pediatric Atlas that I’ve been working on; 3) […]
Posted by pete on July 14, 2014
https://blog.cogneurostats.com/2014/07/14/analyzing-freesurfer-surfaces-with-afnisuma-tools/