The Defense

"In 1594, being then seventeen years of age, I finished my courses of philosophy and was struck with the mockery of taking a degree in arts. I therefore thought it more profitable to examine myself and I perceived that I really knew nothing worth knowing. I had only to talk and wrangle and therefore refused the title of master of arts, there being nothing sound or true that I was a master of. I turned my thoughts to medicine and learned the emptiness of books. I went abroad and found everywhere the same deep-rooted ignorance."

-Van Helmont (1648)


"The new degree of Bachelor of Science does not guarantee that the holder knows any science. It does guarantee that he does not know any Latin."

-Dean Briggs of Harvard College (c. 1900) 

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When I was a young man I read Nabokov's The Defense, which, I think, was about a dissertation defense and the protagonist Luzhin's (rhymes with illusions) ensuing mental breakdown. I can't remember that much about it; but the point is that a dissertation defense - to judge from the blogs and article posts written by calm, rational, well-balanced academics without an axe to grind, and who would never, ever exaggerate their experience just for the sake of looking as though they struggle and suffer far more than everybody else - is one of the most arduous, intense, soulcrushing, backbreaking, ballbusting, brutal experiences imaginable, possibly only equaled by 9/11, the entire history of slavery, and the siege of Stalingrad combined. Those who survive it are, somehow, of a different order.

The date has been set; and just like a real date, it will involve awkward stares, nervous laughter, and the sense that you're not quite being listened to - but without the hanky-panky at the end. The defense is in three days, and part of me knows that most of it is done already; having prepared myself well, and having selected a panel of four arbiters who, to the best of my knowledge, when placed in the same room will not attempt to eat each other. ("Oh come on, just a nibble?" "NEIN!")

Wish me luck, comrades. During the defense, the following will be playing in my head:

Important Announcement from Andy's Brain Blog

Even though I assume that the readers of this blog are a small circle of loyal fanatics willing to keep checking in on this site even after I haven't posted for months, and although I have generally treated them with the same degree of interest I would give a Tupperware container filled with armpit hair, even they are entitled to a video update that features me sitting smugly with a cheesy rictus pasted on my face as I list off several of my undeserved accomplishments, as well as giving a thorough explanation for my long absence, and why I haven't posted any truly useful information in about a year. (Hint: It starts with a "d", and rhymes with "missertation.")

Well, the wait is over! Here it is, complete with a new logo and piano music looping softly in the background that kind of sounds like Coldplay!

For those of you who don't have the patience to sit through the video (although you might learn a thing or two about drawing ROIs with fslmaths, which I may or may not have covered a while back), here are the bullet points:

• After several long months, I have finished my dissertation. It has been proofread, edited, converted into a PDF, and sent out to my committee where it will be promptly filed away and only skimmed through furiously on the day of my defense, where I will be grilled on tough issues such as why my Acknowledgements section includes names like Jake & Amir.

• A few months ago I was offered, and I accepted, a postdoctoral position at Haskins Laboratories at Yale. (Although technically an independent, private research institution, it includes the name Yale in its web address, so whenever anybody asks where I will be working, I just say "Yale." This has the double effect of being deliberately misleading and making me seem far more intelligent than I am.) I recently traveled out there to meet the people I would be working with, took a tour of the lab, walked around New Haven, sang karaoke, and purchased a shotgun and a Rottweiler for personal safety reasons. Well, the Rottweiler more because I'll be pretty lonely once I get out there, and I need someone to talk to.

• When I looked at the amount of money I would be paid for this new position, I couldn't believe it. Then when I looked at the amount of money I would be paying for rent, transportation, excess nosehair taxes (only in a state like Connecticut), shotgun ammunition, and dog food, I also couldn't believe it. Bottom line is, my finances will not change considerably once I move.

• A new logo for the site has been designed by loyal fanatic reader Kyle Dunovan who made it out of the goodness of his heart, and possibly because he is banking on bigtime royalties once we set up an online shop with coffee mugs and t-shirts. In any case, I think it perfectly captures the vibe of the blog - stylish, cool, sleek, sophisticated, red, blue, green, and Greek.

• Lastly, I promise - for real, this time, unlike all of those other times - to be posting some cool new techniques and tools you can use, such as slice analysis, leave-one-out analysis, and k-means clustering (as soon as I figure that last one out). Once I move to Connecticut the focus will probably shift to more big data techniques, with a renewed emphasis on online databases, similar to previous posts using the ABIDE dataset.

• I hope to catch up on some major backlogging with emails, both on the blog and on the Youtube channel. However, I can't promise that I will get to all of them (and there are a LOT). One heartening development is that more readers are commenting on other questions and posts, and helping each other out. I hope that the community continues to grow like this, which will be further bonded through coffee mugs and t-shirts with the brain blog logo on it.

How to Write a Dissertation Prospectus

Before beginning work on a dissertation, one has to put together and submit a prospectus, which is from the ancient Greek pro, meaning "Stuff," and spectus, meaning "One who writes." A prospectus is, in condensed form, what you will be writing about in your dissertation. This provides your dissertation committee, over a period of roughly two presidential administrations, a chance to read a brief, concise, single-spaced 50-page report about whether they should take the trouble to read a future dissertation that, for practical purposes, is measured not in pages but metric tons. Some students, knowing that a picture is worth a thousand words, merely substitute a diagram to helpfully outline what will be covered in their dissertation:

For those of us who aren't savvy enough with Google Images to produce an informative picture, however, we will need to rely on good, old-fashioned scientific prose. But first, let's cover the basic structure of your prospectus. Remember, by following these time-tested principles and recommendations, you will at least somewhat entertain your committee before they reject your dissertation proposal as completely ridiculous and holding about as much scientific merit as a can of Cheez-Whiz.


1. The Cover Page

A strong prospectus starts out with a cover page, containing the title of your dissertation, the names of the members of your dissertation committee, and possibly a dedication to someone who has had an immense and positive influence on your life, such as your parents, your girlfriend, or Tony Soprano. Feel free to embellish your cover page with depictions of cherubs and muses.

Example cover page from Edward Grieg's dissertation prospectus.

2. Personal Photo

Even after four years of working with your adviser, you shouldn't make any rash assumptions, such as that he or she will know what you look like. In order to help out your adviser, you should attach a professionally done personal photo showing you looking as serious and scientific as possible. This can score you major points with your committee, as they will now have a mental image of you as a serious, cultured individual, unlike all the other hirsute weirdos wandering around the department:

Source: Calvin Klein

3. Body of the Prospectus

Once you have successfully completed your cover page and personal photo, you're now ready for the most important and weightiest section of your prospectus - by which I mean, of course, that you actually have to write something related to the work that you have been doing over the past several years. A good prospectus should start out with something that immediately entices and intrigues the reader, such as the following:

Most honorable, sovereign, and magnificent lords,

I herewith enclose the following enclosements; a prospectus designed to please both one's innate curiosity and satisfy his critical faculties, by expounding upon the work of my graduate career, which has definitely involved reading only scientific articles and books, and not bootlegged copies of Humungo Garbanzo BOLD Responses. It is my utmost belief, penetrating my entire being and reaching even so far as the pyloric sphincter, that this prospectus will contribute to the PUBLIC WEAL and common good of academia and the scientific committee, viz., all of you, etc., et al, ora pro nobis.

The dissertation which I hereafter propose is that, in order to determine the neural mechanisms and correlates of prospective model-free decision-making, one must bring to bear several unique methodologies, such as functional and structural connectivity, multivoxel pattern analysis, univariate mastication, seed-based cortical peristalsis, dynamic CSF segmentation and haustral movements, computational modeling region of interest corrected thresholding bread milk Astroglide tortillas refried beans.

Deign, most honourable, magnificent and sovereign lords, to receive, and with equal goodness, this respectful testimony of the interest I take in whatever it is I have been studying the past several years. And, if I have been so unhappy as to be guilty of any indiscreet transport in this glowing effusion of my heart, I beseech you to pardon me, and to attribute it to the tender affection of a true student, and to the ardent and legitimate zeal of a man, who can imagine for himself no greater felicity than to see you happy.

Also, if somehow one of you manages to come across one of my old issues of Humungo Garbanzo stuffed in the back of the lowest drawer of my filing cabinet, I know nothing about that.

Most honourable, magnificent and sovereign lords, I am, with the most profound respect,

Your most humble and obedient servant and fellow-citizen,

Don't worry if you have a difficult time coming up with anything that sounds remotely plausible or scientific; if you've written a prospectus like the one above, odds are that your committee, satisfied that you are fluent in academic bullshit, will stop reading somewhere around the second paragraph, and fail to note that once you ran out of buzzwords you started supplying items from your grocery shopping list.

How I Feel When Writing My Dissertation

I've undergone quite a change in the past couple of months - my voice has deepened, my hips have widened, and those once-nascent dark patches of hair sprouting under my armpits and within my nostrils have now become so thick that they require maintenance at least twice a week with a weed-whipper.

I am referring, of course, to starting my dissertation.

Starting one's dissertation is accompanied not only by physical developments, however, but by drastic psychological changes as well. Such monomaniacal devotion of mental energy to such a specialized area of research studied by literally tens of persons around the world can lead to bizarre alterations in one's perceptions and behavior, including paranoia, cerebral hemorrhaging, grand mal seizures, clubbed fingers, piles, scrofula, scrapie, delusions of persecution, listening to Nickelback, demonic possession, and Nutella-induced comas. All of these symptoms have been declared normal and well within the safety margins of the International Dissertation Committee Panel (or IDCP, pronounced "eye-dick-pee").

In addition, dissertation writers are notorious for their trademark reclusive lifestyle and cantankerous mood. Someone who used to be social and outgoing will now refuse to go out with their friends or interact with anybody, claiming that they have to work on their dissertation. What this really means is that they used to hate everybody anyway, and now they just have a valid excuse for refusing to attend any event that doesn't offer free food.

However, probably the most distinguishing characteristic of a dissertation writer is his inability to talk about anything other than his dissertation; somehow, the conversation keeps coming back to the 200-pound - I mean, 200-page! - gorilla in the room:


BRAD: I'm having a really difficult time right now; my hemorrhoids are acting up again, my hairplugs aren't taking, and last week my parents were brutally murdered.

TOM: I know how you feel; right now I'm writing my dissertation.

BRAD: I'm so sorry.


Even if they don't directly reference their dissertation, you can bet your gorilla that they are worrying about it, constantly. To help you out, here are translations of some oblique dissertation references that you might otherwise miss:

WHAT THEY SAY: I'm going to work for eighteen hours straight today, no distractions whatsoever, unplugging my Internet and turning off my phone and euthanizing my pets, operating only on coffee strong enough to melt through several layers of reinforced steel similar to that one scene with the facehugger blood in the movie Alien.
WHAT THEY MEAN: I'm going to sit around for eighteen hours straight marathoning seasons of Breaking Bad, and probably will spend a grand total of about two hours on my dissertation. And by that, I mean thinking about my dissertation.

WHAT THEY SAY: My life is hard.
WHAT THEY MEAN: I have, quite possibly, the most arduous life in existence. I mean, for example, those people fighting in World War II, yeah, they had it rough, with D-Day and the siege of Stalingrad and everything, but did they have to write their dissertation? No.

WHAT THEY SAY: I'm going to work from home today.
WHAT THEY MEAN: I'm going to do some drugs today.


As we can see, writing a dissertation is a trying experience for any individual, no matter how hurly-burly a soul he or she may be. However, even after the months and years of dissertation writing, even after the numerous and hard-fought battles with one's committee about what studies to run, even after the premature aging leading to whitened hair, strained eyes, and hardened arteries - even after all that, it's worth that moment when half of your four-person committee reads at least a few pages of your dissertation on the day of your defense, looks at you with quizzical expressions usually reserved for grotesque carnival exhibits, and asks you questions that are so unrelated to anything you ever wrote and anything you ever experienced that if you weren't in academia you would swear you were surrounded by certified space loons.

If that still doesn't do it for you, you will still have the ecstatic experience of paying upwards of $2,000 for binding and printing your dissertation (based on your number of dependents and whether you select optional dissertation rhinestone gilding), after which a copy of your thesis will be stored in a remote warehouse in Zimbabwe, along with some extra weed-whippers.


To help you better understand the whole dissertation experience - and keep in mind, I am VERY aware of my audience - I've included the following scene from Metal Gear Solid 4: Guns of the Patriots. In what I believe is a thinly veiled metaphor for dissertation writing, I've broken down what everything means:

Solid Snake: You
Microwave hallway: Dissertation
Crawling through the microwave hallway: Writing your dissertation
Wait, hold on a second here - microwave hallway? That's how the bad guys defend the most valuable part of their fortress? With microwaves?: Yes
Why not machine guns or mines or something?: The game was made in Japan.
Otacon: Your adviser
Extremely awkward camera placement behind Snake's derriere: The extraordinary sense of humility you feel taking part in such a noble enterprise, making an original contribution to the body of knowledge and maybe, just maybe, making the world a better place. Or something. I really had to make a stretch for this one.
Other people: The friends and family in your life who, while you were writing your dissertation, were busy fighting genetically-modified supersoldiers and terrifying biped war machines. Which is what they do anyway.