All posts for the month October, 2013

Using for fMRI analysis

I receive a lot of questions about how to setup the basic analyses in AFNI.  Previously I detailed using, the AFNI graphical user interface to which really does all of the hard work under the hood.  Today I’m going to briefly review the common options in and why I use them.  You […]

Simulating fMRI Designs

I could say a lot about proper simulation of fMRI experiments.  Basically it’s important to measure the efficiency of your design before an experiment (see here).  If you wanted to perform the calculations yourself, MATLAB/Python/Octave are all options and the process is “fairly simple”. Xmat = [design_matrix’ * design_matrix]; main_effects(ct) = [ contrast’ * (Xmat^-1) […]

Adjusting MRI Smoothness for Multi-Scanner Comparisons

Typically when we smooth (aka spatial filter) our fMRI data using a fixed kernel size.  And as we know, the size of a smoothing kernel makes some difference in the final results (see below).  This shows a group analysis map, the results are more shocking on single subject maps. The common misconception is that you […]