Mendeley

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.

A Survey of Methods Reporting

Figure 1: Why you are (probably) a slacker
Taken from Carp, 2012

A recent article in NeuroImage suggests that we cognitive neuroscientists aren't providing our methods in adequate detail when we submit articles for publication. Is it because we're all lazy, shiftless academic scum? Absolutely.

However, that is only part of the problem, according to the publication author, Joshua Carp. Because neuroimaging processing pipelines are so complex and multifaceted, the number of unique ways to process a given set of data rapidly approaches infinity (or at least several thousand). Of course, there are more reasonable ways to analyze data than others; for example, you probably wouldn't want to smooth your data before doing registration, because that would be straight-up bonkers. However, it can be done, and, based on the article, a substantial fraction of studies published from 2007 to 2011 do not provide adequate information for replication, leaving it an open question for whether a failure to replicate a given result represents a failure of the replication study, or whether the initial result was a false positive. Furthermore, this increased flexibility in processing leads to a greater likelihood of producing false positives, and makes it less likely that another lab will be able to reproduce a given experiment (see, for example, Ioannidis's 2005 paper on the subject).

To mitigate this problem, Carp suggests that neuroimagers adhere to the guidelines provided by Russ Poldrack in his 2008 paper, including providing details about number of subjects, number of runs (a surprising amount of studies did not report this, according to Carp), how ROI analyses were performed, how to present results, and so forth. I agree that these are all important things to report, although I also happen to agree with Carp that some of the more technical details, such as signal scaling, are provided as a default in programs such as SPM and often aren't given another thought; whereas something like smoothing, which has a higher likelihood of being changed based on the question being addressed, is more often to be reported. Thus Carp's suggestion that more journals provide a supplementary material section for all of the nitty-gritty details, I believe, is a good one.

In any case, another timely reminder (for me at least) about methods reporting and why it matters.

Unix for Neuroimagers: Shells and Variables

First, a few updates:

1) We just finished our first week of the semester here, and although things haven't been too busy, it may be a couple of weeks before I get back on a steady updating schedule. I'll do what I can to keep dropping that fatty knowledge on the regular, and educating your pale, soy-latte-white, Famous Dave's BBQ-stained faces on how to stay trill on that data and stack that cheddah to the ceiling like it's your job. And if you got one of those blogs dedicated to how you and your virgin-ass Rockband-playing frat brothers with names like Brady and Troy and Jason eating those cucumber salad sandwiches or whatever and you drop a link to this site, I'll know it. You show me that love, and I show it right the hell back.

2) While you're here, how about you donate a piece of that stack to the American Cancer Society. I mean, damn; I'm out there seven days a week on those roads, sweating and suffering, but you - you're at work procrastinating again, wringing your snow-bunny white hands over whether you should drop out of graduate school or just toughen it out and graduate in eight years, and while you're at it possibly take a swipe at that new Italian breezey who just entered the neuroscience program. Donate first, worry about those problems later.

3) We got another performance for you all this November, including Schumann's Adagio and Allegro for cello and piano, Resphigi's Adagio con Variazioni, and the Debussy cello sonata. Time and location TBA. Also, more music videos will be uploaded soon, but while you're waiting, you can listen to the latest Mozart Fantasie in D Minor, which has proved one of my most popular videos to date; last I checked, it had 57 views, which I think qualifies for viral status. We goin' worldwide, baby! World-WIDE!!

4) AFNI tutorials are next on the docket, after wrapping up the intro Unix tutorials for neuroimagers, and possibly doing a couple more FSL tutorials on featquery, FSL's ROI analysis tool. Beyond that, there isn't much else I have to say about it; now that you've mastered the basics, you should be able to get the program to jump through whatever hoops you set up for it and to do whatever else you need. There are more complex and sophisticated tools in FSL, to be sure, but that isn't my focus; I will, on the other hand, be going into quite a lot of details with AFNI, including how to run functional connectivity and MVPA analyses. It will take time, but we will get there; as with the FSL tutorials, I'll start from the bottom up.


Anyway, the latest Unix tutorial covers the basics on shells and variables. Shells are just ways of interfacing with the Unix OS; different shells, such as the t-shell (tcsh) and bash shell, do the same thing, but have different syntax and different nomenclature for how they execute commands. So, for example, an if/else statement in the t-shell looks different from a similar statement in the bash shell.

Overall, there's no need to worry too much about which shell you use, although AFNI's default is tcsh, so you may want to get yourself used to that before doing too much with AFNI. I myself use tcsh virtually all of the time, except for a few instances where bash is the only tool that works for the job (running processes on IU's supercomputer, Quarry, comes to mind). There are lots of tcsh haters out there for reasons that are beyond me, but for everything that I do, it works just fine.

As for variables, this is one of the first things you get taught in any intro computer science class, and those of you who have used other software packages, such as R or Matlab, already know what a variable is. In a nutshell, a variable is a thing that has a value. The value can be a string, or a letter, or a number, or pretty much anything. So, for example, when I type in the command

set x=10

in the t-shell, the variable is x, and the value is now 10. If I wish to extract the value from x at any time, I prepend a dollar sign ('$') to it, in order to tell Unix that what follows is a variable. You can also use the 'echo' command to dump the value of the variable to the standard output (i.e., your terminal). So, typing

echo $x

returns the following:

10

which is the value that I assigned to x.

From there, you can build up more complicated scripts and, by having the variable as a placeholder in various locations in your script, only have to change the value assigned to it in order to change the value in each of those locations. It makes your programming more flexible and easier to read and understand, and is critical to know if you wish to make sense of the example scripts generated by AFNI's "uber" scripts.

With all of the tutorials so far, you have essentially all of the fundamentals you need to operate FSL. Really, you only need to understand how to open up a terminal and make sure your path is pointing to the FSL binaries, but after that, all you need to do is understand the interface, and you can get by with pointing and clicking. However, a more sophisticated understanding is needed for AFNI, which will be covered soon. Very soon. Patience, my pretties.

Andy's Brain Blog Book Club: Essays

Michel de Montaigne (1533-1592)

I readily admit that, of all the current and popular books supposedly relevant to my field of psychology, I find most of them a bore. Take, for example, The Social Animal, by David Brooks. Advertised as an exploration of social and psychological phenomena through the life story of two rather bland individuals, Brooks tries to show us how much of their thoughts and actions are due to their nature, and how much is due to cultural and societal constraints. This has the potential to be interesting, but I found myself putting it down after about a quarter of the way through; I believe the last straw was when Brooks, in a laughable attempt to capture the dialogue of high-schoolers, had one of his characters shout "Yo! Douche-bag!" Give me a break.

As these books have left me unsatisfied, I have found myself driven into the arms of an older but more experienced mistress: Classical literature. In addition to their insights into the capabilities and limitations of human reason and emotion, these works have proved much more acute investigations into human psychology, and as such are more revealing about the human condition.

One of the most accessible works I have found is Montaigne's Essays. Derived from the French word Essai, which literally means "trial" or "attempt", Montaigne developed this genre in order to explore his own attitudes and prejudices on a variety of topics. A brief survey of the titles of his essays gives the reader a good sense of Montaigne's interests, and what to expect from him: On friendship; On drunkenness; On cannibals; On smells; On the habit of wearing clothes; On vehicles; On the art of conversation; All things have their season; On cruelty; On experience; That our actions should be judged by our intentions; On liars; On the education of children; On the uncertainty of our judgment; On the power of the imagination.

On the whole, ordinary yet compelling topics. However, do not let the titles fool you; Montaigne has a habit of digressing into several other related (and unrelated) topics within the same essay, and sometimes will not even address the title of his essay until the very last few paragraphs. As such, the structure and flow of his essays are often unsystematic. While this may irritate some readers at first, it gradually becomes more familiar, then charming, and then is realized as one of the main strengths of his writing. Montaigne's style is informal and relaxed, and during the course of his essays he tends to disclose several personal details about his own life and habits as they relate to the topic at hand; I for one was pleased to learn that the author had the same peculiar reading behaviors that I do, including marking on the first page of a book how long it took to read it from start to finish.

Furthermore, he discourses brilliantly on a range of subjects that, at first blush, may seem rather odd or inappropriate to talk about so bluntly; however, he somehow manages to bring both humor and dignity to the subjects of disease, indigestion, erectile dysfunction, and gallstones. Montaigne is also great for one-liners, and, if you have not gotten into the habit of underlining passages while reading, his essays will compel you to do so. Here are a few of my personal favorites, which will give you a foretaste of his writing (the corresponding essay from which the quote is taken is in parentheses):

"There are some who are tempted by the charm of an attractive phrase to write about something they had not intended." (On the education of children)

"...I do not know whether I would not much rather have produced a perfectly formed child by intercourse with the Muses than by intercourse with my wife." (On the affection of fathers for their children)

"The worth of a soul does not consist in soaring to a height, but in a steady movement." (On repentance)

"...nothing is so likely to throw us into danger as a frantic eagerness to avoid it." (On vehicles)

"If we have known how to live steadfastly and calmly, we shall know how to die in the same way." (On physiognomy) 

 "Do you ask me whence comes the custom of saying 'Bless you' when a man sneezes? We produce three sorts of wind; that which issues from below is too foul; that which comes from the mouth carries some reproach of over-eating; the third is sneezing, and because it comes from the head and is irreproachable, we give it this honorable greeting. Do not laugh at this subtle reasoning; it is said to be Aristotle's." (On vehicles)  

 "Ease of manner and the ability to unbend are the most honorable and fitting qualities in a strong and generous soul." (On experience)

"We are great fools. 'He has spent his life in idleness,' we say, and 'I have done nothing today.' What! have you not lived? That is not only the fundamental, but the most noble of your occupations. 'If I had been put in charge of some great affair, I might have shown what I could do.' Have you been able to reflect on your life and control it? Then you have performed the greatest work of all...Our duty is to compose our character, not to compose books, to win not battles and provinces, but order and tranquility in our conduct." (On experience)

My volume of Montaigne's Essays is about four hundred pages; a comprehensive reading of all of his essays, if we include his lengthy Apology for Raymond Sebond, is likely several times that. No matter; they should be read as he wrote, at leisure and without any definite plan of where to start and where to end. Anyone may profit from picking up and reading any essay at random.

Lastly, those with a scholarly bent may find it of particular interest to read the Essays in conjunction with Pascal's Pensées (Thoughts), for they represent two opposite poles of the human temperament. Montaigne was at ease with uncertainty and doubt; Pascal hated uncertainty, and spent the latter part of his life collecting his Pensées as a sort of ultimate and unassailable apologetic for Christianity. Montaigne styled himself as both a devout Catholic and a skeptic (his famous motto was, "What do I know?"), and was seen as a moderator and as a voice of reason during the religious wars of his time; Pascal was a fanatic who detested compromise. Montaigne did not think highly of his own intellectual gifts (see how often he comments on his terrible memory), and during his lifetime was remembered more as a provincial statesman than as an author; Pascal was one of the greatest mathematical geniuses in history, whose meteoric career saw the development of several groundbreaking laws, theorems, and inventions, including the syringe and the omnibus.

Two very different characters, but both equally fascinating to read; and while Pascal undoubtedly possesses the greater brilliance of the two, Montaigne perhaps has the more attractive mind. In any case, I hope that you find the time to become familiar with both.

Unix for Neuroimagers: Part 2 (More commands, and the PATH variable)

After you have gotten comfortable and (emotionally) intimate with the basic Unix commands for navigating your environment and listing contents of directories, the other essential tools you will need, if you are using a package like FSL, is a working understanding of the PATH variable. It is not critical that you know how to set the path on your own, but it helps to know conceptually what it does, and why the FSL and AFNI people require you to amend it in certain ways when installing their software.

The PATH variable (Most Unix variables are in all upper case; by the way, now might be the time to define what a variable is; it is an object storing a value, such as a number or a word) is a pointer to specific directories in your directory tree, and allows you to execute the programs and binaries within that directory. For example, almost all of the Unix commands you use are in the /bin folder; instead of having to navigate to the /bin folder to execute a certain command, or explicitly type out the full path to a directory where a command is located, the PATH variable will allow you to execute that command from any directory in your environment. For example, typing the command "echo $PATH" in the terminal might return the following list of directories in my PATH (echo is a command to return the output of a command to the command line, and the dollar sign in $PATH signals that PATH is a variable):

/usr/local/bin:/bin:/usr/local/fsl/bin:/Users/andrewjahn/abin

Note that each directory is separated by a colon. This is a Unix convention, and may take some time to adjust your pitiful human eyes to this.

In this example, all of my FSL binaries (or commands, or executables; I use the words interchangeably, although there are differences in meaning) are located in the directory /usr/local/fsl/bin, while all of my AFNI binaries are located in /Users/andrewjahn/abin. Having these directories listed in my path saves me from having to type the entire path to the command. For example, instead of typing:

/Users/andrewjahn/abin/afni

I can just type:

afni

From anywhere in my Unix environment, and the afni command will execute.

A couple of other important topics covered in this tutorial are startup scripts and sourcing. Startup scripts refer to a series of commands that is executed every time you open up a new terminal or a new shell. In this example, I modify the a startup script called .cshrc (CSH stands for the c-shell; RC stands for run command), and add the lines given by the FSL installation instructions. You can add anything else in there as well, including aliases (i.e., alternate and easier to remember names for more complex commands). The point is that everything within this file will be run each time you begin a new Unix session.

The source command is not strictly necessary, but saves you the time from having to close a session and begin a new one in order to execute everything inside the startup file. Just typing in "source .cshrc" from your home directory is enough to execute the file.


Also uploaded recently is another tutorial covering the basic remove and remove directory commands, as well as how to interact with text files from the Unix command line. I mention it in the video, but I will also restate it here: The rm command is extremely powerful, and removes things forever. That's "forever" with an "f". It does not send them to some Recycling Bin or Trash Bin or anything fruity like that; those files are straight up gone, which means that you better know what you are doing before you use it. This is mostly a word of warning to beginning Unix users, although I have torched innumerable datasets in my day through carelessness, maliciousness, or that fitful combination of both that sometimes seizes me in sudden bursts of anti-fMRI fury.

A 21st Century Phineas Gage

Is it wrong that I feel a little rill of excitement traveling down my spine when something like this happens? That I have some morbid curiosity to find out exactly how this young man's terrible misfortune will translate into interesting scientific findings? We have prohibited ourselves from conducting so-called impossible experiments, such as willingly depriving children of any social contact to see the effects on their development, or subjecting someone to a marathon of Jersey Shore reruns, because these would be monstrous and unethical things to do; however, whenever someone has a stroke or injury which destroys part of their brain, we can't help but feel an odd mixture of sympathy for their plight, and the giddy sensation that we have hit a case study jackpot.

The story: A Brazilian construction worker named Eduardo was minding his own business, constructing stuff and whistling at those ripe Brazilian hunnies walking past his construction site, when he was struck by a falling metal rod which impaled the top of his head and partially exited between his eyes.

CT scan showing the metal rod in Eduardo's skull.

Eduardo, being a total boss, remained calm and was able to explain the situation to the doctors. Seeing their shocked expressions, he was even able to joke, "What, do I have something on my face?"

After a five-hour-long surgery, the rod was extracted, and Eduardo did not appear to show any signs of distress, pain, or malfunctioning. The head neurosurgeon also had this to say:

[The head neurosurgeon] said the bar entered a "non-eloquent" area of the brain that doesn't have a specific, major known function. [Eduardo] Leite is expected to remain in hospital for at least two weeks.

I'm not sure what "non-eloquent" means, exactly, but the fact is, that piece of metal took out a large chunk of real estate, and there actually are some specific, major known functions for that part of the brain that just got obliterated. The reason this case is so intriguing is because it closely mirrors an accident which occurred over a century and a half ago: The famous case of Phineas Gage.

Like Eduardo, Phineas was minding his own business, constructing railroads and shouting at those white breezeys, when a small explosion sent a tamping iron through the bottom of his skull and out the top of his head.

Reconstruction of the tamping iron's path through Gage's skull. Given the time period, scientists hypothesize that Phineas' first words were, "Egad!"

The injury blew out most of Gage's left inferior frontal lobe, and observers noted several dramatic changes in his behavior following the incident: He had become more irritable, more impulsive, and appeared unable to manage his day-to-day life as he had done before, supposedly due to an impaired ability to properly evaluate the consequences of his actions. Given this, neuroscientist Antonio Damasio hypothesized that the frontal lobes were necessary for interpreting and regulating emotional states, and for responding to more abstract aspects of decision-making (e.g., the amount of money one would be willing to pay for a given option; Croxson et al, 2009).

In any case, an MRI will be needed to determine the location and extent of the damage, and I am sure that Eduardo will be undergoing a battery of tests to examine any changes in his cognitive or emotional capacities; it will be interesting to see if this adds anything new to what the current lesion studies and non-invasive procedures have revealed about this region (or, more likely, regions). I also propose that, since he has taken one for the team, so to speak, Eduardo should be well-compensated by the scientific community; fifteen dollars an hour for his study participation, perhaps; a swimming pool filled with Nutella; and a harem of the world's finest chicas. It is only right that we give something back to those who have suffered the vicissitudes of fate and have given us something in the bargain.

Link: Iron Bar Removed from Builder's Head

Unix for Neuroimagers (Part 1): Fundamentals

As promised, we have begun a new series of tutorials aimed at the beginning neuroimager, who may think that he can get by without learning any computer science whatsoever. This is, unfortunately, not true, and those who wish to pursue a career in cognitive neuroscience need to at least learn the fundamentals; if not for constructing your own scripts, then at least for being able to understand and interpret what others have done. Those who refuse to go beyond their comfort zone and test the waters of what must seem to them a foreign and unfriendly language, will forever be relegated to pushing the Big Button that executes commands or scripts without really knowing what is going on. To enter this field without a working knowledge of programming is to be partially blind.

To that end, these first few screencasts will guide the beginner over the initial hurdles of navigating their computer environment solely through the command line interface. At the basic level of navigation and file manipulation, some simple analogies can be drawn between typing in commands such as cd and ls, and pointing and clicking within the standard Windows or Macintosh operating systems that most people are used to. However, at the more abstract levels involving if/else statements and for loops, there are no ready analogies I can think of, and at this point the Unix shell must be treated as any other foreign language; the only way to learn it is by doing, and by consistent repetition.

Usually I try to supplement the videos with some written commentary, but in this case, I believe that there is a very good introductory resource already out there, which can be found here. Walking through all of these tutorials will probably take less than an hour, but it is worth coming back to them from time to time to reinforce what you have learned.

For those of you who are new to neuroimaging or programming and may doubt whether it will ever really stick, let me assure you that it will, in time. Five years ago I was engaged in a research project the summer of my senior year; however, I knew nothing about computer programming. Nothing. I had taken a class of Java in high school, but barely managed to scrape by with a B-, and that was with copying all of the homeworks from one of the Asian kids in the class under threat of death. I was so useless, I didn't even know how to use Excel (no lie), and needed my advisor to hold my hand through doing the most basic analyses in SPSS. It was humiliating at first, because I knew that many of my colleagues were well versed in all of these tools which appeared as second nature to them, and I felt as though they looked down upon me as some hateful and nasty piece of filth clinging to the soles of their shoes.

However, over time I came to teach myself, more through necessity than anything else. My first job out of college required the use of Unix, the experience with which I greatly exaggerated to a ridiculous degree in my application (I had skimmed through a 1980 Unix textbook borrowed from the public library, and said that I had "experience" with Unix); and I set about to learn whatever I could and whatever I saw was most needed. What I found was that, out of the vast Pacific of commands and options present in Unix, only a minuscule fraction of them were required to successfully carry out the work that I needed to do. More important was molding my mind to accommodate the language and understand how to think through operations before translating my will into a series of typed commands. If I, who had virtually no programming background, a terrible memory, and the attention span of a bag full of puppies, could learn the basics within a year, then so can you. Persist.

This could be you!

There is no need to go it entirely alone. As with any skill, much of the fruits of your labors and lightning flashes of insight will only come through long and solitary hours of study and practice; however, it is as important to learn how to identify external resources, whether they float within the ether of the Internet or are made incarnate in the large, stinking, fleshy pile of humanity which sits next to you in your laboratory. One particularly useful resource I have found is unix.com, a message board related to all things Unix. More than once have I posted problems which I had been breaking my head against for many hours or days, only to have a complete solution posted within a matter of seconds. As long as you are willing to tolerate a little condescension and can put up with some invisible nerdling berating you for sloppy indentation, you should be able to solve most of your problems quite easily.

Good luck, comrade.

Tips for Graduate Students: Preparing for Qualification Exams

Having recently completed my candidacy exam (or qualification exam, or "quals"), I now feel compelled to share with everyone what I have learned about how to have a smooth, successful exam experience. This is relevant mainly to the exams here at Indiana University, although I hope it will generalize to candidacy exams in other places. This is written with the first or second year student in mind, who has already begun to think about their candidacy exam, but has heard several different opinions on what to expect from it. I implore the reader to purge from his mind everything he has heard, and to start over with a fresh perspective; for his ship will be buffeted to and fro by the crosswinds of contrary opinions, preventing him from reaching the safer shores of conviction and instead leave him to founder and ultimately drown in the sea of uncertainty. (I am a professional blogger; don't try metaphors like this on your own.)

Some background on the IU exams: After completing the second year of the PhD program, students are expected to begin their qualification exams; this is usually during the summer between their second and third years of graduate school, although it can be taken during other semesters in certain circumstances. The exam consists of two portions: A written exam, which in turn consists of three or four papers, with no set standard for length (although the norm is usually from 25-35 pages of text, excluding references); and an oral exam, during which the student defends his or her position in the written papers, and can be asked questions which expand upon material discussed in the papers. Students are usually given three months to complete the written portion, and about three or four weeks after that to prepare for the oral exam.

Given all of this, students may well ask how they should best budget their time. The following tips will help guide the young academic scrote on his hazardous journey:

1) Start Early. As in, start as soon as you get to graduate school. This does not mean you should be formulating your questions years in advance; rather, you should be setting a regular reading schedule for yourself as part of your academic routine. People differ on how many papers is sufficient to read in one week, but it is better to err on the side of depth than of breadth. Some may find the time and willingness to read, on average, one or two papers every day; others may benefit more from focusing on only one or two papers a week. The emphasis is less on cramming as much information as possible into your puny human brain as it is to allow yourself enough time to digest high-quality, relevant articles and review papers which are of interest to you. The ancient Greeks had a term for individuals who read widely but possessed only superficial knowledge; they were called sophomores.

2) Mark Up Your Papers. There is probably some study out there, somewhere, written by some guy with a name like Brad or Troy, which has shown that interacting with your reading material helps you to retain information better. In any case, writing down your thoughts, or merely trying to summarize what the main points of the paper are, is an excellent way to comprehend and remember what you read. It also will help you immensely come qualification exam time, as you will have annotations for key studies that you will be discussing in your papers.

3) Get a Reference Manager Program. The best one I have been able to find so far is Mendeley. It allows you to categorize and organize every single paper you download, as well as open it up in another window as a PDF for annotating. In addition, you can use it to easily insert references into your papers, and change the formatting with only a couple of clicks.

4) Don't Listen to Debbie Downers. These people are usually either depressed, or they despise themselves so much that the only way they can get their rocks off is by infecting you with worry, anxiety, and doubt. Separate the wheat from the chaff - identify those who can give you useful advice about the mechanics about the qualification exam process, and who have success stories that you can emulate. There will generally only be a few of these people who can give you truly useful advice; the rest will bitch about how they never saw the light of day for the entire summer they were doing their candidacy exams, or how they handed everything in at the last minute, and expect you to be impressed.

For God's sake, do not humor them; mock them for their sloppy work ethic, box their ears for presuming that you care about their pathetic life, and pour rage like oil upon their heads for spreading such pernicious nonsense. A full three months is more than enough time to write one hundred pages of summary dressed up in your own personal insight, and should inspire curiosity and eagerness, not fear and dread. If you find yourself unable to make any progress and feel as though you are grinding out pages at a torturous pace, you may want to reconsider why you are doing this in the first place. The writing process should be a natural extension of everything you have observed, felt, and studied during your first two years of graduate school, and possibly even what you learned during your undergraduate years; it should not be seen as a test of your patience. The first way will lead to growth, inspiration, and confidence in your work; the second way lies stagnation, decay, and death.

5) Invest in an ETF. Anyone who tells you to stay out of the stock market is either a charlatan or a fool. These are the best years of your life to begin saving, and you should get on it with a quickness. I will be blunt and say that this will require some measure of self-control and austerity, such as reducing the number of outings to Kilroy's and Night Moves. Furthermore, since you are in academia, do not delude yourself into thinking that you have the ability to research stocks individually. You are suited only for discussion of abstract theories that nobody cares about; you are useless when it comes to practical matters, such as personal finance, or operating a food processor.

Fortunately, brokerage firms have already thought about pathetic creatures like you, and will give you access to trading instruments known as Exchange-Traded Funds (ETFs), which are essentially baskets of stocks chosen to represent a certain sector of the market, such as the manufacturing industry or Nutella & Nutella accessories; at the far end, they can be tailored to closely track entire index funds, such as the S&P 500. Some firms, such as Scottrade, will allow commission-free trading of ETFs, which is a good deal.

However, for those pigheaded enough to assume that their natural brilliance in their field somehow endows them with the temperament to pick individual winners and losers in the stock market, the best piece of advice I can give is to read the book The Intelligent Investor by Benjamin Graham, edited by Jason Zweig. It covers all of the fundamentals of investing, and is an excellent primer for getting up to speed on the terminology and strategies for different types of investors. It also contains this revealing quote:

"If you are not willing to go through the minimal effort of reading the proxy and making basic comparisons of financial health across five years' worth of annual reports, then you are too defensive to be buying individual stocks at all. Get yourself out of the stock-picking business and into an index fund, where you belong."

And that's real talk, bitch.

6) Know Your Audience. The point of qualification exams, as I understand them, is to both educate yourself  and deepen your understanding by focusing on a few topics of interest to you; however, you must also take your committee's views and prejudices into consideration as well. After all, they are expecting to learn something too, and not only through concise reviews and distillations of entire oceans of studies, but rather by seeing how this information is filtered through your own insight, and, consequently, how your opinions and views will add a dimension to the existing literature.

That being said, choose your committee wisely, should you have the option to do so. Furthermore, anticipate how they will react to certain experiments you discuss, and plan how you will address questions that will likely come up. Do not be afraid to cite members of your committee in your papers, given the fact that, since they are on your committee in the first place, they will probably have already published something out there that is relevant to what you are writing about. After all, like Carnegie said, the sweetest sound in the English language is the sound of a person's own name. Also, I am willing to bet that people get a little aroused whenever they see themselves cited by another.

7) Check the Freezer for HotPockets. When was the last time you ate? HotPockets are an excellent way to maintain a consistently high level of energy and provide a compact, delicious source of fuel which will help you to write for long stretches at a time. The bread of the HotPockets can be used by your muscles to help lift entire desks off the ground and slam doors shut; the pizza sauce will lead to longer, more intense, and more satisfying fits of rage; and the protein in the pepperoni will dramatically increase libido and dampen all of your inhibitory mechanisms. I base this on absolutely nothing.

8) Be Confident. Even if you are not naturally confident, fake it. Often people will not care if you trip up on small details, as long as you have a clear idea of where you are headed with your arguments and really believe in your conclusions. Those who exude an aura of confidence, both through the written and oral components of their exam, will elicit a greater measure of respect from their committee and their colleagues than those who timidly venture forth only through a series of half measures and minced steps; and this in turn will lead to a smoother, more productive conversation with your committee when discussing what you wrote.

This is a problem I have observed much more in girls than in guys in an academic setting. During public speaking events, for example, girls, for whatever reason, are more likely to preface what they say with namby-pamby phrases like "Now, I really don't know much about this, but...". This enrages me to no end, and if anything, instead of making listeners back off and cut the speaker some slack, encourages them to pile it on and try to trip up the speaker even more. Play pussy, get fucked.

Summary: Qualification exams are a source of much fear and stress, but it need not be so. By starting early and thinking critically about the papers you read and how they fit into your interests, you can stay ahead of the curve and build up an impressive library of fully annotated and organized papers before you even start writing. Tailoring your writing to your audience, as well as making wise investment decisions and satisfying your nutritional needs through HotPockets, will turn you into an unstoppable force of nature.

How I Feel When A Paper Gets Surprisingly Good Reviews

Lesion Studies: Thoughts

(Note: I recently completed my candidacy exam, which involved writing a trio of papers focusing on different aspects of my research. Most of this post is cannibalized from a section I wrote on lesion studies of the anterior cingulate cortex, which produce counterintuitive results when contrasted to lesions of other areas, such as the DLPFC and OFC, which do indeed seem to disrupt the processes that those regions are implicated in from the neuroimaging literature.

My work primarily involves healthy people with intact brains, and observing indirect measures of neural firing through tracking slow blood flow changes in the brain. However, "activation" as defined by fMRI is not the same as the underlying neural dynamics, and, barring invasive single-cell recordings, we have few options for directly measuring neural firing in response to different tasks and psychological contexts. This caveat inherent in fMRI research becomes particularly important when interpreting the results of lesion studies.) 

Although the majority of the neuroimaging literature has implicated the dACC as playing a critical role in the signaling for cognitive control when necessary, the most direct test of a brain structure’s necessity in a cognitive process is through examining subjects presenting with lesions in that part of the brain. For example, if it can be demonstrated that a subject without an ACC still performs equivalent to controls on tasks involving cognitive control, then that would argue against the necessity of that area’s involvement in the hypothesized cognitive process. Studies involving human subjects with lesions are relatively rare and suffer from low power, but can still reveal important aspects of neural functioning.

The ACC, in particular, has been the subject of several lesion studies that have shown conflicting and counterintuitive results. For example, a single-subject lesion study of a patient with left ACC damage exhibited both smaller ERNs and increased RT in response to incongruent stimuli in a spatial Stroop paradigm. This study showed that conflict monitoring and error detection, at least in this patient, do not both come from the same area of ACC, suggesting that these processes occur in different areas. However, while the ERN was shown to be attenuated in the patient, the conflict response (a waveform called the N450) was actually enhanced (Swick & Turken, 2002). This suggests that conflict monitoring occurs in a nearby prefrontal area, such as the DLPFC, before information about the conflict is sent to the ACC.

Figure of the lesion for the single subject analyzed by Turken & Swick (2002). Overlaid are coordinates of peak activation for conflict-related tasks from other studies.

On the other hand, a lesion study conducted by Fellows & Farah (2005) compared the performance of individuals with dACC lesions to that of controls across a battery of tasks hypothesized to involve cognitive control. These tasks included a Stroop task and a go-nogo task which are known to elicit significantly greater increases in RT after errors, and to induce significantly greater amounts of errors during incongruent trials. The results showed no significant interactions between group and task, suggesting that the dACC is not necessary for the implementation of cognitive control. Furthermore, the authors pointed out that tasks involving cognitive control may be confounded with emotional responding, which in turn could simply be associated with the ACC's involvement in regulating muscle tone. In any case, it is apparent that although this structure is somehow associated with cognitive control, it is not strictly necessary for it. 

Figure showing group overlap of lesions in the Fellows & Farah (2005) study.  Circles and squares represent an overlay of a meta-analysis by Bush et al (2000), with circles representing peak activations for cognitive tasks, and squares representing peak activations for emotional tasks.

Comparison of Stroop effect (measured in percent signal change from mean congruent trial RT) and error rate between lesion patients and controls. No significant difference was found on either measure between the two groups.

In sum, these lesion studies suggest that the dACC may not be indispensable for signaling the DLPFC to implement cognitive control. However an alternative explanation is that patients with ACC lesions are usually ipsilateral, and that furthermore they may be compensating for required cognitive control by recruiting nearby cortical areas. However, two lines of evidence argue against this interpretation. First, one of the lesion patients examined in the Fellows & Farah (2005) had extensive medial ACC damage encompassing dACC bilaterally, but showed a similar pattern of error rates and RT difference between congruent and incongruent conditions as did the other lesion patients and the control group. Secondly, lesion studies of other areas of the brain – such as the orbitofrontal cortex – have shown that those regions appear to be specific to the cognitive processes they are hypothesized to be involved in. For example, patients with OFC lesions exhibit significantly impaired performance in decision-making tasks such as the Iowa Gambling Task and Wisconsin Card Sorting Task, as well as decreased autonomic activity in response to highly risky gambles (Bechara et al, 1994). Even though the patients in this study had suffered from their lesions for a comparable amount of time as the lesion subjects in the Fellows & Farah (2005) study, there was no evidence of recruitment of other cortical areas in order to support their deficits in decision-making.

However, although these lesion studies have shown no significant differences in error rates between the lesion patients and controls, other experiments have revealed that patients with ACC damage are less likely to correct for their mistakes on trials immediately following an error. In addition, patients with ACC lesions are less likely to be aware that an error has occurred (Swick & Turken, 2002). These results suggest that there may be a necessary role for of the ACC for the actual detection of errors, which would be consistent with the hypothesis that this area is involved in the comparison of actions against their predicted outcomes. How lesions affect the transfer of information from the ACC to the DLPFC and other cortical regions supposedly involved in the implementation of cognitive control, however, is less well understood.

Bottom line: If the inferences from neuroimaging studies are to believed, then the ACC is necessary somehow for cognitive control or executive function; however, lesion studies belie this claim, suggesting perhaps that the necessary processes for these cognitive functions take place elsewhere and merely light up the ACC as some sort of epiphenomenon. Admittedly, I am unsure of what to make of all this. The most useful experiments to carry out, in my opinion, would be to apply transcranial magnetic stimulation (TMS) to temporarily knock out this area in healthy controls, and then observe what happens; however, as TMS is only able to disrupt neural firing on surface areas of the cortex, stimulation of deeper areas remains impractical. With continuing advances in the ability of TMS to stimulate deeper cortical (and, possibly, subcortical?) structures, we may get a better grasp of what is going on.

Miles for Lyle

Readers and fellow brain-bloggers,

In a couple of months, I will be running the Milwaukee Lakefront Marathon as a fundraiser for the American Cancer Society (ACS). This is the first time I have done something like this, and I am going to need all the help I can get.

Over a year ago, my grandpa was diagnosed with Merkel cell carcinoma, a particularly malignant and aggressive form of cancer which has since spread to his liver. Needless to say the prognosis is not good; but instead of sitting around on my hands worrying, I took advice from a friend and decided to try raising money through the sport that I love.

Lyle Oechsle - my grandpa - has spent the last couple of decades working as the director of the YMCA in Grand Forks, North Dakota. Some of my fondest memories as a child were going with him to family swim on Friday nights, then cruising over to TCB to the motherfucking Y to load up on that froyo, renting a movie, and falling asleep in front of the fire we would build in the fireplace downstairs. Reader, these were some of the happiest years of my life; having a stable routine and something to look forward to every weekend with someone who cares about you.

Me and Lyle enjoying a grill

Lyle was also highly sensitive to the needs of others, and I remember accompanying him on several occasions to visit his older friends and acquaintances who were suffering from disease of coping with the loss of loved ones. I didn't understand how important it was at the time that these people had someone who would visit them regularly or leave them presents; but it made me aware of what many people go through, and it put things in perspective for me all these years later.

And now, it is my turn to take care of him. Please visit the following webpage and, if you are willing and able, make a donation for whatever you can spare: Miles for Lyle

Get at that money!!

aaand, We're Back

I'm back from my vacation to Minnesota and ready to grind out some more posts to educate the filthy, teeming swarms of graduate students seeking to find out everything they can about neuroimaging, and also to get my paper up.

Speaking of which, you may notice that there are now advertisements on the sidebar and at the bottom of the blog. This wasn't a hijack by Google, but something I decided to implement, given a growing readership base and the increased production of educational tools and videos. For example, all of the FSL videos were recorded using a trial version of Camtasia 2, which I plan to buy; to help defray the costs, every once in a while drop a mouseclick on the customized ads which use highly sensitive personal information encoded on your web browser's cookies to scream at you that there is a babe stampede of Christian/Atheist/Buddhist singles available in your zip code ready to hook up right the hell now. Every little bit helps.

Also, I'd like to extend a big thank all of you who have posted comments on the videos asking more in-depth questions about different parts of modeling and the processing stream. It's good to see people getting involved and challenging me to answer questions I haven't thought of before; even better will be to get other viewers to share their knowledge and answer questions as well. This is all part of my vision to make the learning part of neuroimaging more interactive, more fun, and more dynamic in response to questions as they pop up. The existing message boards for the top three packages (SPM, FSL, and AFNI) are great tools to use, and I hope to complement them with screencasts which address questions as they come up, and to show, step by step, how to approach problems and how to learn the basics. I realize that there are only a handful of views on the tutorials so far, but I hope that they have been helpful, and that I haven't spread too much misleading information.

As mentioned previously, within the next couple of weeks I hope to create a small series of Unix and programming tutorials aimed at getting the beginning neuroimager off his feet and able to use the FSL and AFNI tools with confidence and elan. The ultimate goal being, of course, to get to the level where you can impress all those ripe hunnies in the lab with your technical know-how and insightful critical thinking skills. (That's the reason anybody does this, right?)

On Hiatus

I will be gone for the rest of this week, returning next Sunday. Cheers everyone!

The Horror: Wagenmakers Goes RealTalk On Social Psychology

There will always be men destined to be subjugated by the opinions of their century, of their Country, of their Society: Some men today act the part of the Freethinker and the Philosopher who, for the same reason, would have been but fanatics at the time of the League.
--Rousseau, Preface to First Discourse

Computational modeler and miniature golf champion Eric-Jan Wagenmakers recently penned a short essay on a recent series of unfortunate events which have left social psychology with its fair share of bruises and black eyes. While social psychologists may tell you that they just fell down the stairs, the real cause of these contusions, says Wagenmakers, is more systemic.

First, flagship social psychology journals such as JPSP refuse to publish replication studies which can refute existing studies - an important scientific correction mechanism if there ever was one. This has led to the continued credibility of controversial studies such as Daryl Bem's famous (infamous?) precognition experiment, with studies reporting a failure to replicate these results being summarily rejected; apparently, unless a study can add something besides a failure to replicate, it is deemed unfit for publication. It would seem that providing evidence against an established theory would be valuable enough in and of itself, but the guidelines of some of the major journals say otherwise.

Second, there was the high-profile case of Diederik Stapel, a social psychology researcher who may have fabricated data affecting over thirty experiments. Cases of massive fraud are not specific to social psychology by any means - take Marc Hauser in evolutionary biology, for example - but it certainly doesn't help, especially in a field dealing with sensitive social and political topics which are likely to receive more attention from the public.

Third, eminent social psychologist John Bargh published a not-so-nice critique on a group of researchers who failed to replicate one of his experiments, as well as the journal which published it (PLoS ONE) and a commentator who covered the story. (A post about the event can be found here; it looks as though the original post by Bargh was deleted.) The ad hominem attacks employed by Bargh serve as an example of what not to do when someone fails to replicate your study; after all, replication is one of the pillars of scientific investigation. We're dealing with falsifiable hypotheses here, not instant Gospel every time a big name publishes a result. (I would, however, try to make an argument about how Bargh couldn't help writing that response due to uncontrollable external forces.)

Fourth, scientists in the social and cognitive neuroscience fields are very good at obtaining the result that they want, whether they are aware of it or not. According to Wagenmakers: "...If you set out to torture the data until they confess, you will more likely than not obtain some sort of confession – even if the data are perfectly innocent." This is absolutely true, at least in my own experience. Usually I don't even realize when I am doing it. For example, I'll look at a few dozen different uncorrected voxel thresholds, in order to get it just right so that those two clusters are just touching so that they can pass a certain correction threshold; until I realize that, baby, those aren't activation blobs on my computer screen I'm looking at - it's specks of Cheetos dust. (Don't tell me this hasn't happened to you!)

Thus, the obvious corrections to all of the above are: 1) Journals should be more accepting of replication studies, in order to provide more incentive to replicate and also to mitigate the file-drawer problem; 2) Don't commit massive fraud and ruin the careers of your students and colleagues (but if you do, don't get caught); 3) If someone can't replicate your results, keep it civil; and 4) Make the switch to Wheat Thins. No, wait! What I meant was, try to set a standard of what you will do for your analysis, and adhere to that analysis plan. Wagenmakers recommends trying pre-registration of your experiment online, similar to what is being done with clinical work at the NIH; you may be surprised at how your analysis turns out. Whether the surprise will be good or bad is another matter.

Anyway, I recommend giving the original article a read; what you've just read is an inferior version of his prose. Also, Wagenmakers and Michael Lee have posted a free pdf of how to do Bayesian data analysis; I recommend taking a look at this as well, in case you are curious.