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.
NIH Talk: Distinct Regions of mPFC Process Pain and Cognition
Grown-ups like numbers. When you tell them about a new friend, they never ask: "What does his voice sound like?" "What games does he like best?" "Does he collect butterflies?" They ask: "How old is he?" "How many brothers does he have?" "How much does he weigh?" "How much does his father make?" Only then do they think they know him. If you tell grown-ups, "I saw a beautiful red brick house, with geraniums at the windows and doves on the roof..." they won't be able to imagine such a house. You have to tell them, "I saw a house worth a hundred thousand francs." Then they exclaim, "What a pretty house!"
--Saint-Exupery, The Little Prince
I often have vivid fantasies about how my talks will be received: The audience will laugh at my jokes; listen in attentive silence about the obstacles I overcame to carry out my research; gasp in astonishment as I reveal my big finding which will change the field forever. And, at the end of my talk - concluded with a germane and heartfelt anecdote which ties everything together - an ocean-like roar of applause and yells as I am lifted up high on a chair and carried through the streets with great honor. The men shake my hand vigorously and the ladies kiss me on the cheek. "Hats off, gentlemen!" says the town crier, "A genius!"
For some reason, and much to my dismay, reality fails to match my heart's desires. The jokes and asides feel flat and fall stillborn from my mouth. The background of my study feels less like an epic and more like reciting a laundry list. (I swear it sounded much more interesting when I was rehearsing it to myself.) Any small issue with the projector cutting out or with my Powerpoint animations failing to work, in the moment feels as embarrassing and indecent as being caught with my fly unzipped.
But I keep going nonetheless, holding out hope to someday achieve that perfect talk combined with the perfect moment. The ultimate trade awaiting the ultimate practitioner.
In any case, something to strive for.
Video Introduction to ROI Analyses
About forty years ago certain persons went up to Laputa, either upon business or diversion, and upon their return began to dislike the management of everything below, and fell into schemes of putting all arts, sciences, languages, and mechanics upon a new foot. To this end they procured a royal patent for erecting an Academy of Projectors in Lagado. Every room hath in it one or more projectors. The first man I saw had been eight years extracting sunbeams out of cucumbers.
--Swift: Gulliver's Travels, Part III, chs. 4-5
I'm updating my videos on fMRI basics, starting with ROI analysis. This is low-hanging fruit, yes, but delicious fruit, fruit packed with nutrients and sugars and vitamins and knowledge, fruit that will cure the scurvy of ignorance and halt the spreading gangrene of frustration.
In these videos you will observe a greater emphasis on illustration and analogy, two of the most effective ways to have concepts like ROI analysis take root inside your mind; to make them have a real, visceral presence when you think about them, and not to exist merely as words that happened to impinge on your retina. These videos take longer to make, but are all the more rewarding. And if they help you to think differently than you did before, if they help you, even without my knowing it, to see the world as I understand it, then I will have taken a significant step toward fulfilling my purpose here on this earth.