Dissertation Defense Post-Mortem

A few weeks ago, I mentioned that I had my dissertation defense coming up; understandably, some of you are probably interested in how that went. I'll spare you the disgusting details, and come out and say that I passed, that I made revisions, submitted them about a week and a half ago, and participated in the graduation ceremony in full regalia, which I discarded afterward in the back of a U-Haul truck for immediate transportation to a delousing facility located somewhere on campus. Given that I was sweating like a skunk for nearly three hours (Indiana has quite a few graduates, it turns out), that's probably a wise choice.

For those who need proof that any of this happened, here's a photo:

I believe this conveys everything you need to know. Also, it costs considerably less than paying for the professional photos they took during graduation. Don't get me wrong; the ceremony itself was an incredible spectacle, complete with the ceremonial mace, tams and tassels and gowns of all fabrics and colors, and the president of the university wearing a gigantic medallion that makes even the most flamboyantly attired rapper look like a kindergartener. Even for all that, however, I don't believe it justifies photos at $50 a pop.

Currently I am in Los Angeles, after an extended stint in Vancouver Island visiting strange lands and people, touring the famous Butchart Gardens, and feeding already-overfed sea lions the size of airplane turbines. Then it's back to Minneapolis, Chicago, and finally Bloomington to pack up and leave for the East Coast.

Comprehensive Computational Model of ACC: Expected Value of Control

Figure 1: Example of cognitive control failure

A new comprehensive computational model of dorsal anterior cingulate cortex function (dACC) was published in last week's issue of Neuron, sending shockwaves throughout the computational modeling community and sending computational modelers running to neuroscience magazinestands in droves. (That's right, I used the word droves - and you know I reserve that word only for special cases.)

The new model, published by Shenhav, Botvinick, and Cohen, attempts to unify existing models and empirical data of dACC function by modifying the traditional monitoring role usually ascribed to the dACC. In previous models of dACC function, such as error detection and conflict monitoring, the primary role of the dACC was that of a monitor involved in detecting errors, or monitoring for mutually exclusive responses and signaling the need to override prepotent but potentially wrong responses. The current model, on the other hand, suggests that the dACC monitors the expected value associated with certain responses, and weighs the potential cost of recruiting more cognitive control against the potential value (e.g., reward or other positive outcome) for implementing cognitive control.

This kind of tradeoff is best illustrated with a basic task like the Stroop task, where a color word - such as "green" - is presented in an incongruent ink, such as red. The instructions in this task are to respond to the color, and not the word; however, this is difficult since reading a word is an automatic process. Overriding this automatic tendency to respond to the word itself requires cognitive control, or strengthening task-relevant associations - in this case, focusing more on the color and not the word itself.

However, there is a drawback: using cognitive control requires effort, and effort isn't always pleasant. Therefore, it stands to reason that the positives for expending this mental effort should outweigh the negatives of using cognitive control. The following figure shows this as a series of meters with greater cognitive control going from left to right:

Figure 1B from Shenhav et al, 2013
As the meters for control signal intensity increase, so does the probability of choosing the correct option that will lead to positive feedback, as shown by the increasing thickness of the arrows from left to right. The role of the dACC, according to the model, is to make sure that the amount of cognitive control implemented is optimal: if someone always goes balls-to-the-wall with the amount of cognitive control they bring to the table, they will probably expend far more energy then would be necessary, even though they would have a much higher probability of being correct every time. (Study question: Do you know anybody like this?) Thus, the dACC attempts to reach a balance between the cognitive control needed and the value of the outcome, as shown in the middle column of the above figure.

This balance is referred to as the expected value of control (EVC): the difference between control costs and outcome values you can expect for a range of control signal intensities. The expected value can be plotted as a curve integrating both the costs and benefits of increased control, with a clear peak at the level of intensity that maximizes the difference between the expected payoff and control cost (Figure 2):

EVC curves (in blue) integrating costs and payoffs for control intensity. (Reproduced from Figure 4 from Shenhav et al, 2013)

That, in very broad strokes, is the essence of the EVC model. There are, of course, other aspects to it, including a role for the dACC in choosing the control identity which orients toward the appropriate behavior and response-outcome associations (for example, actually paying attention to the color of the stroop stimulus in the first place), which can be read about in further detail in the paper. Overall, the model seems to strike a good balance between complexity and conciseness, and the equations are relatively straightforward and should be easy to implement for anyone looking to run their own simulations.

So, the next time you see a supermodel in a bathtub full of Nutella inviting you to join her, be aware that there are several different, conflicting impulses being processed in your dorsal anterior cingulate. To wit, 1) How did this chick get in my bathtub? 2) How did she fill it up with Nutella? Do they sell that stuff wholesale at CostCo or something? and 3) What is the tradeoff between exerting enough control to just say no, given that eating that much chocolate hazelnut spread will cause me to be unable to move for the next three days, and giving in to temptation? It is a question that speaks directly to the human condition; between abjuring gluttony and the million ailments that follow on vice, and simply giving in, dragging that broad out of your bathtub and toweling the chocolate off her so you don't waste any of it, showing her the door, and then returning to the tub and plunging your insatiable maw into that chocolatey reservoir of bliss, that muddy fountain of pleasure, and inhaling pure ecstasy.

Andy's Brain Blog Advice Column: Should You Date In Graduate School?

Dear Andy's Brain Blog,

I am midway through the second year of my graduate program, and over the past couple of months I have gotten to know a girl in my cohort very well. At first we started just by hanging out a lot, but one night we both got pretty jacked on some Nutella spiked with Smirnoff Ice and before I knew it things got out of control. It quickly escalated into kissing, necking, holding hands, and heavy petting, although we kept it PG (-13). Although I had the time of my life that night, and although I have had this same scenario happen with several girls before, something feels different about this one; it doesn't feel like just another fling, but possibly the prelude to a full-on relationship. 

However, I am conflicted: How much should a man dedicate himself to a relationship, if at all, when there are the pressing concerns of classes, teaching, writing, and research? Would it be best to break it off before it becomes too serious? Or, if it is to be pursued, how should it be approached?



Dear Brad,

Let me begin by stating it is perfectly normal, and not weird at all, for a manboy of your age to begin experimenting with odd cocktails of sugary products. But first let me address an unasked question: Why should you trust me with relationship advice? Well, not to brag or anything, but I have run a (half) marathon, I have no major diseases, and I have read over a dozen novels, including the complete oeuvre of Laura Ingalls Wilder and Beverly Cleary. The depth and breadth of my reading, combined with extensive travels throughout the upper American Midwest and two provinces of Canada, has granted me unique insight into prepubescent sororal relationships, the finer points of horse trading, and how to recover from crop damage following a hail storm. Most important, I have become an observant scholar of relationships between the sexes - as Tolstoy would put it, the tragedy of the bedroom - and this endeavor has granted me an eagle-eye view over the landscape of your squalid desires.

To illustrate the deleterious effects of falling in love, a peculiar phenomenon of which you seem to be at risk, I share with you a letter - ladies and gentlemen, an honest-to-god, handwritten letter! As though you need any more evidence of the madness wrought by such primitive emotions - recently received from one of my colleagues at a neighboring university which described his sinking into the turbid ocean of his own lust, the unfortunate result of a series of trysts and resulting hanky-panky with a post-doctoral student working in another lab, which, instead of draining the cisterns of his lust, whipped him into a frenzied passion. Besides the irritation provoked by the omission of any question as to how I was doing - the letter was, in a sense, one prolonged, histrionic soliloquy directed toward an uninterested audience - I was shocked to hear of the level of absorption and mindless passion to which he had fallen (he would have said risen). He enumerated, in painstaking detail, the features and mien of his lover; the slender, supple, opalescent skin of her bare arm; those vermilion, pillowy, textured lips rising to meet his upon awakening from a fitful, sleepless night; and above all, serving as two bright nodes in a trinity of passion, a pair of milky peaks bedighted with brilliant orbs; incarnadine, inexhaustible wellsprings of his bliss, the very thought of which was enough to send a rill of excitement down his spine and terminate in a limpid jet of love.

Exhibit two has no ocular evidence, but rather rests on a memory; old, but still intolerably vivid. An acquaintance of mine in college, living in an adjacent room, once let down his guard and fell completely, hopelessly, stupidly in love with one of the first girls that he met. He once had the gall to stop me on my way out the door to a morning class merely to tell me of his first kiss shared with the object of his desire; he described how, as they talked one night, he had gradually pulled her closer to him, as if by the force of God, and how she began to talk more rapidly and at a higher pitch the closer they were drawn together, before a brief and pregnant silence; and then - a thousand comparisons between the expectation and the reality, a bubble of ecstasy bursting in slow motion - their lips met.

After that, he was a changed man; his grades went to pot, he claimed to see the world in a different light, and he began to go so far as to read and write poetry under her intoxicating influence. It was, from my perspective, a silly and infantile episode in his life; and lest the reader think that this was some innocent, puppy-love affair, let him know that I was, on several occasions, rudely awakened early in the morning by the sounds of strenuous intercourse. After they broke up - as inevitably happens under the demands and expectations of such powerful emotions - he was a wreck for months. His personal hygiene fell into desuetude, his appearance became slovenly and repulsive, and one could see, at a glance, that where he was once brimming with untamed eros, he was now spiritually detumescent. I hardly talked to him since that catastrophic episode, although one time he did manage to corner me and, still under the influence of a fevered mind, tell me that what had transpired - kiss, relationship, breakup, all - was one of the best things that happened to him. To this day, I cannot help reflecting on that puerile outpouring without a feeling of contempt.

As has been shown, love can lead to such dangerous feelings as inklings of the Eternal or the Infinite, along with all of their concomitant inspirations to do simultaneously heroic and stupid things; feelings that there might be, in fact, a deeper and greater reality beyond the pale of the daily grey. All of this, of course, is pernicious nonsense, and should be avoided accordingly. And, lest anyone forget, falling in love also leads to a pathological form of self-forgetfulness, spawning powerful and conflicting emotions such as a deep concern for someone other than the self, painful feelings of both tenderness and possessiveness, and the stirrings of insensate jealousy. How is it, I ask, that any serious student is supposed to concentrate on their work with all of these inchoate feelings spurring them to blind insanity?

However, if you have already crossed the Rubicon and find yourself increasingly enthralled to another, there is still hope to break the emotional ties before they become so entwined with your own being that to sever them would be, in effect, an amputation of the soul. After all, what the composers and poets and painters seldom mention is that, in the beginning at least, one can fall out of love as quickly as they fall into it; and I therefore recommend that, during one of your more lucid moments of reasoning - perhaps when the clouds of your mind have been dispelled after a particularly vigorous congress - it would be both fitting and proper to bring up a sensitive topic likely to introduce divisions between you and your lover; politics and religion being the two examples that most readily come to mind, although I am sure you can find others. It is best to exploit these divisions early on, as I have observed several miscarriages of the natural order of relationships in which two individuals, having known and cared for each other for several years, no longer find these differences to be grounds for breaking up, nor do they even find these differences to be of much importance at all; instead, these differences are seen petty and trivial compared to the emotional and physical well-being of their partner.

By all means, do not let this happen to you. Reader, I have seen men and women worked up into a passion - literally, a sensuous passion, far more intense than that effected by the most possessive jealousy or the most animal lust - over differences such as those described above. For maximum effect, of course, it is helpful to have an entire group of people, and instead of a difference per se, have them all hold more or less the same opinion in solidarity against an invisible opponent; as I have observed such groups, with their perceived moral superiority and righteous indignation serving as a highly volatile fuel, require only the faintest of sparks to overthrow their vaunted reason and ignite a general conflagration of directionless emotion. I once read somewhere a dull intellectual describe such events, in which each individual has a similar opinion, lightly adopted but firmly held, as arising from a combination of ignorance, dishonesty, and a pusillanimous desire for social acceptance; but in any case, the point here is to tap into that same atavistic, tribal mentality, in order to alienate and distance yourself from another, lest you find yourself so emotionally involved with this person that you are unable to easily assign them to a category.

In all, best to nip this in the bud straightaway, and immerse yourself in your readings, research, and teaching, lest you lose sight of what is really important. Relationships, love, marriage, et al. is for saps, as is self-evident to any reasonable observer; and if any of this is to be engaged in at all, it should only be for health purposes, without any resulting attachment, similar to a day at the spa. One of my friends recently sent me a copy of a book called The Red and the Black, by a man named Stendahl, saying that it would help me understand such trivialities; but in my hands, it was merely a lump of valuable matter. I hear that several young readers entering college are beginning to 'discover' Stendahl; I wish them joy.


One of the most useful resources I have yet found for organizing and annotating papers is the reference manager Mendeley. Mendeley's incredible powers are self-evident; only mere months ago I was surrounded by towering stacks of papers, feeling guilty that I had massacred countless trees in order to produce reams of articles that I would never get around to anyway. Then I found Mendeley, burned all those papers with extreme prejudice (what else can you do with a stack of papers you don't want to read?), and haven't looked back. Now, instead of wasting money on pens, paper, and highlighters, every paper I have ever read is at my fingertips as long as I have a computer and an Internet connection. Now, instead of hazarding the inability to read my chicken-scratches that I wrote down months ago on a sheet of paper, I have everything typed up nice and legible. Now, instead of feeling like just another dweeb whose desk space is swamped with more than he can handle, providing visible proof of his incompetency and slovenliness, I can hide that dweebiness down, deep down, where nobody can ever find it.

Mendeley has a host of features, many of which are documented on their website; I will only mention a couple here that I find particularly useful. First, in addition to inserting and formatting references into word processors, Mendeley also features an intuitive interface and allows the user to organize papers quickly and easily.

Mendeley Interface. Folders are on the left; list of returned search items in the middle; reference information on the right.

However, in my experience the most useful feature is Mendeley's built-in PDF reader, which opens up articles in a separate tab for easy reference. The paper can then be marked up with annotations, notes, and highlights, which is useful for writing down your deepest thoughts, feelings, and musings on complex yet beautiful scientific topics.

Papers can also be shared with groups of coworkers and friends through Mendeley's online sharing system, which works quite smoothly. Share those papers, even with people who don't want them or haven't even asked for them, and feel a sense of satisfaction that you are doing something good for someone else.

Let me share a personal habit. In my most private moments, when the air is so still you can hear the sound of the lid of a jar of Nutella being unscrewed, where the only smell is the faint odor radiating from my socks, and when I am absolutely sure nobody is watching, I select multiple references using the shift key and then insert them into a Word document. Try it.

FSL Tutorial 2: FEAT (Part 2): The Reckoning

(Note: Hit the fullscreen option and play at a higher resolution for better viewing)

Now things get serious. I am talking more serious than the projected peak Nutella in 2020, after which our Nutella resources will slow down to a trickle and then simply evaporate. This video goes into detail about the FEAT stats tab, specifically what you should and shouldn't do (which pretty much means just leaving most of the defaults as is), lest you screw everything up, which, let's face it, you probably will anyway. People will tell you that's okay, but it's not.

I've tried to compress these tutorials into a shorter amount of time, because I usually take one look at the duration of an online video and don't even bother with something greater than three or four minutes (unless it happens to be a Starcraft 2 replay). But there's no getting around the fact that this stuff takes a while to explain, so the walkthroughs will probably remain in the ten-minute range.

To supplement the tutorial, it may help to flesh out a few concepts, particularly if this is your first time doing stuff in FSL. The most important part of an fMRI experiment - besides the fact that it should be well-planned, make sense to the subject, and be designed to compare hypotheses against each other - is the timing. In other words, knowing what happened when. If you don't know that, you're up a creek without Nutella a paddle. There's no way to salvage your experiment if the timing is off or unreliable.

The documentation on FSL's website isn't very good when demonstrating how to make timing files, and I'm surprised that the default option is a square waveform to be convolved with a canonical Hemodynamic Response Function (HRF). What almost every researcher will want is the Custom 3 Column format, which specifies the onset of each condition, how long it lasted, and any auxiliary parametric information you have reason to believe may modulate the amplitude of the Blood Oxygenation Level Dependent (BOLD) response. This auxiliary parametric information could be anything about that particular trial of the condition; for example, if you are showing the subject one of those messed-up IAPS photos, and you have a rating about how messed-up it is, this can be entered into the third column of the timing file. If you have no reason to believe that one trial of a condition should be different from any other in that condition, you can set every instance to 1.

Here is a sample timing file to be read into FSL (which they should post an example of somewhere in their documentation; I haven't been able to find one yet, but they do provide a textual walkthrough of how to do it under the EV's part of the Stats section here):

10  1  1
18  1  1
25  1  1
30  1  1

To translate this text file, this would mean that this condition occurred at 10, 18, 25, and 30 seconds relative to the start of the run; each trial of this condition lasted one second; and there is no parametric modulation.

A couple of other things to keep in mind:

1) When setting up contrasts, also make a simple effect (i.e., just estimate a beta weight) for each condition. This is because if everything is set up as a contrast of one beta weight minus another, you can lose valuable information about what is going on in that contrast.

As an example of why this might be important, look at this graph. Just look at it!

Proof that fMRI data is (mostly) crap

These are timecourses extracted from two different conditions, helpfully labeled "pred2corr0" and "pred2corr1". When we took a contrast of pred2corr0 and compared it to pred2corr1, we got a positive value. However, here's what happened: The peaks of the HRF (represented here by the timepoints under the "3" in the x-axis, which translates into 6 seconds (3 scans of 2 seconds each = 6 seconds), representing the typical peak of the HRF after the onset of a stimulus) for both conditions were negative. It just happened that the peak for the pred2corr1 condition was more negative than that of pred2corr0, hence the positive contrast value.

2) If you have selected "Temporal Derivative" for all of your regressors, then every other column will represent an estimate of what the temporal derivative should look like. Adding a temporal derivative has the advantage of accounting for any potential lags in the onset of the HRF, but comes at the cost of a degree of freedom, since you have something extra to estimate.

3) After the model is set up and you click on the "Efficiency" tab, you will see two sections. The section on the left represents the correlation between regressors, and the section on the right represents the singular value decomposition eigenvalue for each condition.

What is an eigenvalue? Don't ask me; I'm just a mere cognitive neuroscientist.
For the correlations, brighter intensities represent higher correlations. So, it makes sense that the diagonal is all white, since each condition correlates with itself perfectly. However, it is the off-diagonal squares that you need to pay attention to, and if any of them are overly bright, you have a problem. A big one. Bigger than finding someone you loved and trusted just ate your Nu-...but let's not go there.

As for the eigenvalues on the right, I have yet to find out what range of values represent safety and which ones represent danger. I will keep looking, but for now, it is probably a better bet to do design efficiency estimation using a package like AFNI to get a good idea of how your design will hold up under analysis.

That's it. A few more videos will be uploaded, and then the beginning user should have everything he needs to get started.

Repost: Why Blogs Fail

Pictured: One of the reasons why blogs fail

Blogger Neuroskeptic recently wrote a post about why blogs fail, observing what divides successful from unsuccessful blogs, and why the less successful ones ultimately stop generating new content or disappear altogether. Reading this made me reflect on why I started this in the first place; initially it was to write down, in blog-form, what I saw and heard at an AFNI workshop earlier this spring. Since then, I tried to give it a more coherent theme, by touching upon some fMRI methodology topics that don't get as much attention as they deserve, and creating a few walkthroughs to help new students in the field get off the ground, as there isn't much out there in the way of interactive videos showing you how to analyze stuff.

Analyzing stuff, in my experience, can be one of the most intimidating and paralyzing experiences of a graduate student's career; not because of laziness or incompetence, but because it is difficult to know where to start. Some of the obstacles that hinder the analysis of stuff (e.g., common mistakes involving experiment timing, artifacts that can propagate through an entire data set, not having a method for solving and debugging scripting errors) do not need to be repeated by each generation, and my main objective is to point out where these things can happen, and what to do about them. Of course, this blog contains other topics related to my hobbies, but overall, the theme of how to analyze stuff predominates.

In light of all of this, here is my pact with my readers: This blog will be updated at least once a week (barring any extreme circumstances, such as family emergencies, religious observations, or hospitalization from Nutella overdose); new materials, such as walkthroughs, programs, and instructional videos, will be generated on a regular basis; and I will respond to any (serious) questions posted in the comments section. After all, the reason I take any time out of my busy, Nutella-filled day to write any of this content is because I find it interesting and useful, and hope that somebody else will, too.