Jörn Alexander Quent's notebook

where I share semi-interesting stuff from my work

A way to get MNI coordinates for subcortical voxels of a CIFTI file

What do I want to do? In this post, I will demonstrate how it is possible to use the R packages cifti and ciftiTools to get the MNI coordinates of the subcortical voxels in your CIFTI file. This table can then be used to select voxels based on their coordinates and do further things with them like creating masks. Read more →

Understanding the basics of the general linear model (GLM) in the context of fMRI

Prelude Sources that I found useful General libraries Simple linear regression Multiple linear regression Special cases One sample t-test Two sample t-test Paired t-test Two-way ANOVA Does the contrast weighting matter for the test-statistics? Covariance matrix of the residuals A example design matrix for fMRI Multiple testing problem Calculate FWE FWE correction Random field theory Permutation tests FDR Conclusion Glossary Prelude I was revisiting some of the basics surrounding fMRI especially the GLM and contrasts. Read more →

Matlab function to create stacked texture maps for Unity

I’ve been experimenting with different materials and shaders in Unity recently. One problem is that especially if you want use the same texture for the same large object you get these nasty tiling effects: Luckily, I found this obscure shader on Unity’s GitHub page, which is amazing but it asked for something called a map texture, which took me ages to figure out. Read more →