I watched an episode of The Big Bang Theory last night where Dr. Sheldon Cooper was airing an episode of “Fun with Flags,” which gave me the idea for today’s blog post title. A while ago, I detailed how to create ROIs in AFNI using a variety of different methods. And I even included a […]
All posts in category Neuroimaging
Fun with AFNI Masks
Posted by pete on August 16, 2013
https://blog.cogneurostats.com/2013/08/16/fun-with-afni-masks/
Multiple Basis Functions with afni_proc.py
Admittedly the title is a little bit opaque, you can already use afni_proc.py to have some of your regressors use the GAM basis function and others to use another basis function (e.g. SPM). But one thing that I find helpful is to compare a standard basis function (e.g. GAM, SPM, SPMG2, etc) with an FIR […]
Posted by pete on August 14, 2013
https://blog.cogneurostats.com/2013/08/14/multiple-basis-functions-with-afni_proc-py/
Analyzing ERP Data with PCA-ANOVA in R
Running a PCA-ANOVA in R is fairly straightforward. In this post we’ll focus on doing a temporal PCA on clusters of ERP channels. First you will want to arrange the data in one file. If you are coming from Net Station, you can export your ERP averaged files to text and then use MCAT to create […]
Posted by pete on August 5, 2013
https://blog.cogneurostats.com/2013/08/05/using-r-to-do-pca-anova-pt1/
Tips for Remote Processing
Quite a few tools for processing MRI data take considerable amounts of time to run, even with computer hardware getting faster and cheaper daily. I have previously discussed how to queue up multiple Freesurfer jobs with GNU Parallel in order to automatically queue and dispatch a number of Freesurfer processes simultaneously. But what do you […]
Posted by pete on July 29, 2013
https://blog.cogneurostats.com/2013/07/29/tips-for-remote-processing-of-mri-data/
Creating Volume ROIs in AFNI
For those keeping track at home, an ROI involves selecting a section of the brain (or subset of voxels) that you have some interest in. The ROI can be a geometric shape or drawn by hand. It can be defined by anatomical markers or by functional activation or really by anything you want. AFNI has […]
Posted by pete on July 24, 2013
https://blog.cogneurostats.com/2013/07/24/creating-volume-rois-in-afni/