All posts for the month August, 2013

Analyzing DTI Data in AFNI (Part 2)

I previously described how to do some DTI analyses in AFNI.  To review, we could use a linear alignment to the b0 image in order to correct for some eddy current distortions.  There is also the option of aligning the data to the individual subject’s high-resolution anatomical data.  Whenever you do a motion correction, it’s […]

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 […]

Fun with AFNI Masks

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 […]

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 […]

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 […]