AFNI already has a host of programs that use R to analyze MRI data – 3dLME, 3dMVM, 3dMEMA, etc. Suppose you wanted to create your own functions that use R to manipulate data – well here’s a quick introduction. In this quick example, here is how to “Auto Mask” your dataset in R. source(‘path/to/AFNI/AFNIio.R’) thedata […]
All posts in category MRI
Using R with AFNI
Posted by pete on April 9, 2013
https://blog.cogneurostats.com/2013/04/09/using-r-with-afni/
A better way to run AFNI’s uber_subject
I used to use fink, and then I switched to MacPorts; truthfully, neither of them really made me happy. Now I mostly use homebrew, and one real advantage (besides being faster and lighter weight) is that it’s very easy to get AFNI’s GUI programs up and running on a Mac. Install AFNI (you’ve probably already […]
Posted by pete on April 8, 2013
https://blog.cogneurostats.com/2013/04/08/a-better-way-to-run-afnis-uber_subject-p/
Dropping file extensions
Randomly, for those people who do a lot of manipulation of file names, it can be painful to constantly use sed or awk or basename to change the filename without the extension. Here are three options to copy a file via 3dcopy (part of AFNI, works just like cp, but for image files, will also […]
Posted by pete on March 19, 2013
https://blog.cogneurostats.com/2013/03/19/dropping-file-extensions/
Converting DICOM files to NIFTI
Most people who are processing MRI/fMRI data will need to convert data from the scanner format DICOM to a more usable NIFTI format that is used by a variety of neuroimaging software packages (e.g. AFNI, FSL, SPM). As with most things in neuroimaging, there are a variety of options and here are a few (though […]
Posted by pete on March 18, 2013
https://blog.cogneurostats.com/2013/03/18/converting-dicom-files-to-nifti/
Correlating Brain and Behavior in AFNI
If previous posts hadn’t given it away, AFNI is my tool of choice for processing neuroimaging data. A lot of people get confused on the sheer number of options there are and that most things can be accomplished in a variety of ways. Today I’m going to outline three ways of doing Correlations between fMRI […]
Posted by pete on March 8, 2013
https://blog.cogneurostats.com/2013/03/08/correlating-brain-and-behavior-in-afni/