This tutorial is about objects - the building blocks of an experiment. E-Prime uses object-oriented programming, which means that the user selects pre-designed objects from the E-Prime toolbox, and then arranges and modifies them to suit his experiment.
Read moreIntroduction to E-Prime
Over the next two weeks I'll be posting a series of videos on how to use E-Prime, by creating a Stroop experiment using building blocks known as objects. These objects have attributes, or properties, that determine object characteristics such as shape, duration, and color. Through arranging objects a certain way and modifying their properties, you can create a wide variety of experiments.
Read moreReverse Normalization of fMRI Data
Normalization - the transforming of data to a standardized space - is a common preprocessing step, and for good reason: it allows us to perform group analysis; it reduces variability in the size and shape of the brain images; and it allows for comparisons across studies by putting the data into a standardized space. Five millimeters to the left and ten millimeters to the rear of the anterior commissure then becomes same location from one study to the next.
Read moreExtracting Timecourses with 3dmaskdump
ROI analysis often means averaging over all the voxels within a mask - either the average parameter, or the average timeseries. For most researchers this is all they need.
Whether or not that applies to you as well, I would like to talk about one more type of ROI analysis: extracting data from each voxel. Most researchers use this analysis to extract the timeseries for each voxel in the brain, although you can extract whatever data you like - parameter estimates, timeseries, and anything else contained in your voxels.
Read morefMRI Lab: ROI Analysis in FSL
By now you should begin to see common themes in each of the videos: We create masks using either spheres or an atlas; we extract data from those masks using whichever tool is most appropriate for the software that you're using; and you can analyze the extracted numbers with whatever statistical software you like.
Read moreABB Podcast #3: Ken Pugh (President, Haskins Laboratories)
This week we talk to Ken Pugh, president of Haskins Laboratories, about reading disorders, the brain, and whether neuroimaging can treat and diagnose dyslexia.
fMRI Lab: ROI Analysis with AFNI
I'm updating some of the old videos I had on ROI analysis, this time with AFNI. I'm trying a new format, in which I have a separate video introducing the topic (in this case, ROI analysis), and then a "lab" video or two showing how to do it in different software packages. I'm trying to have the intro videos be on the shorter side, around 5 minutes, while the lab videos are a little longer and more in-depth, around the 10-minute mark. I hope the figures and animations make this technique more understandable.
Read moreComments Section Upgrade
Hey all, we've upgraded our comments section to Disqus! This makes it easier to follow threaded comments, and also allows you to uploaded images of whatever you have a question about - making it easier for me (and others) to help you out.
Read moreABB Podcast #1: Jay Van Bavel (NYU)
Our first podcast is now up! Powerful, hard-hitting interview with Dr. Jay Van Bavel about social media, Trump's Twitter account, and Unabomber copycats. A must-listen for anyone exercising or traveling roughly thirty minutes or less.
New Website
I am happy to announce the official migration of Andy's Brain Blog to the new website, andysbrainblog.com! I hope that the layout is easier to use and easier to read; as always, if there are specific features that you would like - such as upgrading the comments to Disqus, or having a list of tags you can use to filter posts - let me know in the comments section below.
I hope you enjoy the new site, and I look forward to hearing from you all!
Sincerely,
Andrew Jahn, Ph.D.