Creating videos of anatomical images

If you have a 3D anatomical image (dicoms) of you brain, here's a really easy way to make it into a movie. Thought this would be a fancier thing to send to participants as opposed to the boring fslview screenshot :). Information courtesy of Sylvia Morelli:

1. Download this program and install on your computer

2. Open up Osirix. Import all the dicoms into Osirix.

3.  Click on the name of the patient/participant.

4.  In the top panel, there is a button called “Orientation” with the three views of the brain. You can click on whichever view you want.  I generally like saggital.

5. Then, go to file —> “Export to movie” or there is a button that says “Movie Export” in the top right hand side of the toolbar.

6. You can do this for each Orientation and create three different movies.  

There's also some fancy 3D rendering stuff that I haven't had a chance to check out - maybe I'll update this blogpost when I do! Have fun!

Explaining Culture, Sperber 1996: Book Summary

I just finished reading Dan Sperber’s Explaining Culture (1996), and have to return it to the library soon – so I thought I would digitize some of the reading notes I had jotted down. Overall, I thought the ideas were really cool. I’ve always been interested in concepts like culture, shared reality, collective memory etc, so this book was really up my alley. If anything, it game me the vocabulary to talk about the relationship between psychology, sociology and anthropology. To be clear, this isn’t really meant to be a review of the book as much as a summary of what I thought were the mains points.

The central idea of the book is to study culture as an epidemiology of representations, and to think of population-scale macrophenomena as the cumulative effect microprocesses that bring about individual events. In the context of culture, these microprocesses are the instances of inter-individual information transmission, which are in turn constrained by individual mental processes (i.e. human cognition). That is to say, cultural transmission involves the interplay of different ecological (i.e. writing, oral) and psychological (e.g., memory) processes.

There are two types of representations – mental representations and public representations. Public representations are often manifestations of mental ones. More crucially, because mental representations are private and tied to the individual, a mental representation has to be transformed into a public representation before it can be transmitted. Hence, each transmission is associated with a transformation, which leads to many opportunities for “mutations”. This is somewhat different from genetic transmission, which often has high fidelity between generations. In Sperber’s words – communication is transformation, not replication.

To push the analogy to diseases even further, there are cultural endemics (traditions) and epidemics (fashion). Cognitive processes are the different pathologies. Thus each phenomenon can be different, with different explanations. The task is to explain the distribution of representations, and not necessarily each representation. What ties the study of culture together isn’t so much having the “same mechanisms”, but rather the general approach, the types of questions asked and the ways of constructing concepts.

A representation is defined by two things – the object that it represents, and the information-processing device that processes the representation. It is important to consider the material properties of representation, because they have different effects on cognitive processing. While anthropology has focused on the causal explanation of cultural facts, and psychology has focused on the study of conceptual thought processes. The study of culture has to bridge these two frameworks, and seek to understand the psychological susceptibility to different cultural phenomenon.

On this note, Sperber makes the distinction between dispositions and susceptibility. Dispositions are adaptations (that were selected for by evolution). Susceptibility is the side effects that come with dispositions. In particular, meta-representational ability is a human disposition, which in turn makes us susceptible to cultural representations. It allows us to doubt and disbelief, but also allows us to suspend doubt and disbelief.  For example, our meta-representational ability allows us to learn half-understood ideas that build on things that are better understood. This has interesting implications for religious beliefs, where we temporarily suspend our disbelief based on respect for authority.

Sperber proposes two mechanisms for transmission – communication vs. imitation. Here, we are more interested in communication. He argues that the spread of ideas via communication should be thought of more as a process of attraction, rather than a process of selection. The outputs of which are not solely determined by inputs, but also on constructive cognitive processes that transform the inputs in a systematic, predictable way.

The last few chapters deal with the modularity of the mind, and argue that the mind is likely modular, and cultural diversity is compatible with a modular mind.

My Workview

This quarter, I'm taking this rather interesting class called "Designing the Professional". Full course description here:

ENGR 311B: Designing the Professional

How to Get a Life as well as a PhD: Seminar open to ALL doctoral students (Humanities, Sciences and Engineering). Apply principles of design thinking to designing your professional life following Stanford. Topics include: Introduction to "design thinking", a framework for vocational wayfinding and locating profession within life overall; tools to investigate multiple professional paths. Creation of personal "Odyssey Plan" to innovate multiple prototypes for post-PhD professional launch.

Terms: Spr | Units: 1 | Repeatable for credit | Grading: Satisfactory/No Credit

Instructors: Evans, D. (PI) ; Sheppard, S. (PI)

So far, it's been fairly thought-provoking. To document these thoughts, I felt that it would make sense to blog my assignments here - otherwise, I'll probably lose them by next quarter. The assignments might also be of us of readers who are interested in thinking about their "work-life". Hopefully Dave won't sue me for copyright infringement on his homework. Here's the first assignment:

Write your Workview (150 words - or so)

A workview would address the critical issues related to what work is and means to you. It is not just a list of what you want from or out of work, but a general statement of your view of work. Schumacher's definition of a "theory of work" is one example.  A workview may address such questions as:

• Why work?
• What's work for?
• What's it mean?
• How does it relate to the individual, others, society?
• What defines good or worthwhile work?
• What does money have to do with it?
• What does experience, growth, fulfillment have to do with it?
• Does a PhD have a special form or work, and if so how?

What we're after is your philosophy of work - what it's for,  what it means.  It's essentially your work manifesto.  When using the term "work" we mean the broadest definition - not just what you do to make money or for "a job".  Work is your active engagement with the world and can extend well beyond a narrow definition of job or labor or even career.  Work is the largest single component of most people's waking lives.  Over a lifetime it occupies more of our attention and energy than any other single category.  Accordingly we're suggesting you take the time and reflection to articulate what work and vocation mean to you (and perhaps what you hope it means for others as well).

People's workviews range widely in what they address and how widely they incorporate issues related to service, others, the world, standard of living, growth, learning, skills/talents, etc.  We want you to address what you think is important (i.e., the questions listed above).  While not prescribing that you address the question of service to others/the world or explicit connection to social issues or your higher values, we do findthat we concur with Martin Seligman (who you're reading this week).  He found that the people who do make an explicit connection between their understanding of work in general, and a job or role in particular, are more likely to find satisfaction and meaning in their work and are more enabled to adapt to the inevitable stresses and compromises that come with being engaged in the world.  Since satisfaction and meaning-making are things most of our students tell us they long for, we encourage you to explore those questions.

My Response

We each find meaning in our lives in different ways. For me, I derive meaning from my relationships with those close to me, and the work that I do. Work is not merely any activity that I do, but one that demands commitment, requires sustained effort and comes with a certain set of responsibilities. My criteria of good work is inspired by the neurosurgeon Wilder Penfield, who in considering possible careers, measured them up against the following criterion – “to support myself and my family, and somehow make the world a better place in which to live”.  I read his autobiography in college, and this simple criterion has stuck with me since. Financial remuneration is important to me for two reasons: (i) it is external validation that my work is valued, and (ii) it provides me with the means to support me and my family. It does not have to be much, but it should be enough to provide my children with the comforts and opportunities that I had growing up. In addition, good work should make a positive, concrete contribution to society.

Given the philosophy of work described above, I try to see my time as a PhD student as a career and a calling. However, this can be burdensome during the times when career prospects seem bleak or when the work does not feel meaningful. During those times, I consciously switch to thinking of my PhD as a job, and that helps me get through the day. That said, the switch feels like holding my breath under water – I can only do it for that long before having to resurface to breathe again.  

Web Resource for Young Scientists (Undergraduate and Up)!

Timeless Pieces
You and Your Research
Richard Hamming

Undergraduate Research 
College - What I did right and where I screwed up?
DJ Strouse

Applying to Grad School

Get into grad school for science, engineering, math and computer science
Matt Might

How to get a great letter of recommendation
Matt Might

Guide to Applying to US Science PhD Programs and Fellowships
DJ Strouse

Choosing a Lab and Applying Successfully
Maya Schuldiner

Succeeding in Grad School
How to Succeed in Graduate School: A Guide for Students and Advisors? 
Marie desJardins

How to Choose a Good Scientific Problem
Uri Alon

After Graduate School
YoungPIForum, Weizmann Institute of Science
http://www.weizmann.ac.il/YoungPI/

FSL Tips

Automatic Atlas Query

If you need a table with the coordinates and atlas labels of clusters in a nifti map, check out this script written by Brainder. In his words, any information that is not shared is lost, so I hope he doesn't mind me sharing his script here.

Colorbars

To make colorbars for your figures when using fslview, navigate to: /usr/local/fsl/etc/luts (or wherever you save your FSL directory), and find colorbar.nii.gz. Open that file in fslview and you can change the colors to the ones matching your figure. Then screenshot the image.

fslorient2std
Very often, the files you obtained from the scanner are oriented in a weird way, and are incompatible with the MNI152 Standard Template Image used in registration. Use this command to reorient the image so that they appear the "same way round" in FSLVIEW (note, your original images do have to have the correct header information)

Face Stimuli

Thinking of running a psychology/neuroscience study with faces as stimuli? Here are some face databases:

NimStim Set: http://www.macbrain.org/resources.htm
* Hmm, I find the photos a little weirdly cropped. The hair looks really strange.
* If you find the faces strange, it usually helps to morph several faces together (e.g., using Fantamorph).

Karolinska Directed Emotional Faces (KDEF): http://www.emotionlab.se/resources/kdef

Chicago Face Database:
http://faculty.chicagobooth.edu/bernd.wittenbrink/cfd/index.html

• 158 photographs of Black and White individuals. Targets are represented with the following expressions:
• neutral
• angry
• happy (with open mouth)
• happy (with closed mouth)
• fearful

Settling into Grad Student Life at Stanford (August 2014)

I've received quite a few helpful tips as I settled into life at Stanford... I thought I would take a few minutes to write some of them down, in case they may be of use to "future generations". Note that this information is accurate as of August 2014!

Checking-in Early - I arrived a couple of days earlier than the designated check-in date. I wrote in to housing, and they were kind enough to let me check-in a day earlier... In general, I've found the housing staff to be quite helpful and friendly. So if there's anything you need from them, I would say to not hesitate to ask (nicely).

Arrival at the Airport - Take the supershuttle. The cheapest option (shared mini-van) is fine. Stanford discount available here. You shouldn't have to wait more than 20 minutes. The shuttle is parked on the 3rd floor at a curb across the road. If in doubt, just ask the information center, they'd know.

Dorm Essentials - Online shopping ftw.
Google Shopping Express provides one-day delivery for pretty much everything you need. Currently, they only service Bay Area (including Stanford), SF, LA, and Manhattan. The way this works is that when they receive you order, they'll hop onto an environmentally friendly Toyota Prius, go to the respective stores (e.g., Target, Walmart), pick up the stuff, and drop it at your place, *on the same day*. In other words, you can check into your housing residence in the morning, find out your mailing address (housing won't release your mailing address before you check in), and have pillows and sheets shipped to you by 9pm. How cool is that! If you sign up now, you get 6-month trial membership that includes free delivery. Note that this service is currently in beta-testing stage... I really hope it won't go the way of Google Reader (i.e. discontinued)

There's of course also Amazon Student, which lets you get Amazon Prime free for 6-months. The service is pretty similar to Google Shopping Express, except it's next day delivery. In general though, I think you are more likely to find esoteric items on amazon then google express.

Soap.com (and sister sites): 3 months of free next-day shipping on all household items you could possibly need. Likely to be cheaper than Google Express

Craigslist - Doesn't require an introduction

SUpost - Craigslist in the Stanford area. Useful for dorm-essentials, bikes and cars.

Food!
Online shopping ftw again. Amazon Fresh Food provides same day delivery of meat and produce. DashFood delivers from restaurants, including one Singaporean Restaurant!

Transportation 
Car Rentals: ZipCar

BikeShop: I bought my bike at the Campus Bike Shop at Tresidder Union. It was a little pricey, but it was the most convenient option.... Plus, the SUID Card office is on the second floor of Tresidder Union, so I managed to do both things at once on the first day of arrival.

International Students Loan Closet
If you are an international student, be sure to check out the international students loan closet. They loan out a lot of household items, for as long as you are on campus, for a nominal registration fee of $10. Look at what I got!

The loan closet is in the basement of Abrams, EV. But you'll have to make an appointment first at the I-Center.

How to get to the DMV by public transport
If you do not have a US license, you'll need to schedule an appointment with the DMV to take a written test, as well as a behind-the-wheel driving test. The international center has pretty good information on this, so I won't repeat it here.

If you have a US license, but from another state, you will not have to take the behind-the-wheel driving test, but you do need to take the written test. Making an appointment will save you quite a bit of time, but appointments fill up ~3weeks in advance, so you'll have to plan ahead. I didn't make an appointment, went to the DMV when it opened and there was already a line outside o.O. Though I was in-and-out of there in 2 hours, so it isn't too bad really. Make sure you have all your documents (I-20, I-94, passport and out-of-state license) when you are there!

There are two DMVs near Stanford - Redwood City & Santa Clara. Both are really easy to drive to... but Redwood City is more convenient via public transport. For Redwood City, take the Caltrain (from Palo Alto or California Avenue), alight at the Redwood City Station and walk 12 minutes to the DMV.

For Santa Clara, you can take bus 22 from El Camino.

Musings
1. Most things can be accomplished online. There seems to be no need to head out to shopping centers anymore. I'm not sure if that's a good thing.

2. Paradox of choice - with so many options, I feel compelled to look up all of them and find the best buy, which is incredibly difficult with different packaging, sizes, quality etc. I also feel obliged to read the reviews, and people can have such different opinions. Ugh, I hope this doesn't mean I spend all the time saved from going shopping in front of the computer.

Acknowledgments
A lot of the above information came from Erika Weisz, who has been immensely helpful as I settle into Stanford :)