Depth of a culture

I am notoriously unpopular for my pro-American attitude partly because of my blunt straightforwardness which might be considered extreme. While different people I argue with have different reasons to find faults with American culture some say their culture is not deep and is superficial and materialistic.

See, cultures that are based on or adapt modern science are bound to be like that. In fact the materialism is what separates impulsive judgements from rigor of the reasoning. Sure impulsive judgements might be handy at times but more often than not they are are not dependable with the given size of human population and scale of interaction on the planet.

Older cultures obviously are not based on modern approach to reasoning and tend to associate mysterious depths to understanding of life etc. Thanks to the western influence on the approach of reasoning we have tools to embrace uncertainties in a much better way. Why should we take that embracing uncertainty is a good thing? See, this is based on western influence and western cultures have had to evolve under harsher conditions of life because of climate and landscapes etc. Tropical countries naturally support life without requiring much effort from the human side at least not on the scale needed in colder climates. Well why we do we need to live in harsher climates? Well as I said before the size of human population you know, we can not cram lot of people in one place without dropping the individualistic animal instincts within us. Why do you think western influence resonates with many modulo survival fears!

Embracing uncertainty can seem to be superficial but actually it's deeper on the scale that actually matters for survival. It might seem majority of American export being "service" is superficial but re-think and adjust your views. They know how to run empire at least without repeating mistakes (on a relevant time scale). One can ask why am I so certain about my views. It's mainly because one has to instantiate at a certain level otherwise there won't be any objects of decision and I instantiate (am certain) where there is representation/room for uncertainty.

Obviously America is a big country and I don't have samples of interaction from all of it but from east coast which I believe is the strength of the US in causal terms. Coasts stimulate not just America but most countries on the planet so no big surprise. My experience in the mid-west through Madison also reinforces my hypotheses but I am glad and grateful I experienced east coast first as there are many local optima that can make people get stuck in mid-west type areas.

Steps to install Shogun

Shogun's a huge collection of machine learning tools implemented in C++ and wrapped for MATLAB use. With help of Chris Hinrichs I started using the package for my work in DTI classification. They keep coming up with new version every so often and I needed a lookup place for the set of steps to perform. It is linux based software and it's not as simple as double clicking a setup.exe

So here's the steps assuming you have limited access on the machines:

1. Download the latest release from http://svn.tuebingen.mpg.de/shogun/releases/ (As of today the latest version is 0.9.1)
2. cd download_dir/src
3. ./configure --interfaces=libshogun,libshogunui,matlab --destdir=install_dir --prefix=local -enable-glpk
4. make
5. make install
6. Edit .bash_profile in your $HOME directory to add the following line export LD_LIBRARY_PATH=/lib:install_dirlocal/lib:$LD_LIBRARY_PATH
7. In your MATLAB code: addpath('download_dir/src/matlab')

Look into download_dir/examples for examples.

Happy new year

Today marks the beginning of 2010 and a new 10
Approaching the teen years of 21^st century
Makes me both happy and wary
Happy because we seem to be on the road to recovery
Wary because we can't be complacent too early
For the dynamics of our entropy are too hairy

On a personal level I hope
Everyone can at least glance
At romance
For an awesome blissful trance
That can fuel
One to reach your crowning jewel

The journey of romance
Might not all be rosy
Well what else worthy
Can one get without being risky?

At any rate
Here's the poem I wrote
For a new year
Summarizing my newest experiences in the previous year

Refreshing creativity

I found this post on the math prodigy,Terence Tao's, blog. If not for any of the content just the creativity of using English can get attention and trigger some useful empathy. Creative communication is very refreshing to me!

Consistent performance

I have been in the trance of watching a really great movie, Avatar, since last after noon! See I like Hollywood movies for their outpouring risks that show up as variety and quality! I liked Terminator 1 and 2, True Lies, Titanic and have had great opinion for James Cameron. Now after watching Avatar in 3D IMAX I became a life-long fan of James Cameron. All the movies I mentioned have been a "world wide phenomenon" in movies. There is one other James I really admire: James Horner! The score of A Beautiful Mind has a long lasting impression on me and the score of Avatar is excellent!

See producing something great is great but consistency in it is what really impresses me!

CAMINO-TRACKVIS

I have been using CAMINO and TRACKVIS since mid-summer and along the way I built some in-house utilities that I thought should share with DTI researchers. I had written the utilities in C using malloc for memory management but that type of management didn't scale for over million tracts. Then Maxwell Collins suggested to using the "piping management" employed in CAMINO. He then extended and made my code into "releasable format" so in addition to being able to download the utilities package from here, you can also download it from SourceForge and it has been posted to NITRC for review. Below I am pasting the "public description" that I entered while submitting to NITRC.

With increasing efforts on brain connectivity analyses it becomes important to have tools that can allow increased interoperability among different tractography tools. This package allows interoperability between CAMINO and TRACKVIS. CAMINO is a leading software package in DTI processing. The package is from University of College London. TRACKVIS is a tract visualizing utility with capability of visualizing up to and over a million white matter tracts seamlessly. The package is from Massachusetts General Hospital.

The tools in this package allow conversion of tracts from one format to another in a very effective way with ability to handle over a million tracts.

I plan to release some more tools soon.

Military and free market

The two most important (overriding) systemic forces are military and then free market. Free market has some influence on military but the latter overrides in case of a dead lock. There might be (are?) other meta-forces that actually "cause/control" these but these are the objective forces that can be manifested to actually make a difference in the living. It does help to detour (as long as the objective is kept in mind) into some of the spiritualities to have some entanglement effects on the forces but it's hardly replicable or communicable. One has to figure ones own way by honing the empathetical skills which are more or less like theorem proving skills in terms of communicability.

More grease and more

Yesterday I posted a small demo.m. Today I made another small demo.m to convert ROIs in NIFTI format to text files based on a request from my mentor Moo K. Chung, which reminds me also to point to another piece of source code I worked on for Cosine series based representation of white matter tracts.

As I mentioned in my previous post I will soon release CAMINO, TRACKVIS interoperability tools.

Switching gears

I posted a few times based on my encounters in brain image analysis at the Waisman center. Today I wanted to post a sample demo script on reading output from DTI_TK in MATLAB. Then I realized I will wrap the demo script in a meta post about how important it is to be able to switch gears (if one wants to reduce overhead in interdisciplinary research) not only in terms of conceptualizations but simple things like being able to use multiple platforms and software packages. Since I joined Waisman, I got more comfortable with MAC, LINUX etc. I am no longer just a WINDOWS person although I still cannot trade WINDOWS for any other platform. I plan to release some tools for CAMINO TRACKVIS interoperability as well.

See, all research in interdisciplinary at some level and needs ability to switch gears but applied research just has higher demand (for doing noticeable (even locally) research) on the gears and needs sufficient investments in greasing it properly. I worked on projects in collaboration with Psychology departments before while I was at Temple. I interacted with "psychologists" working on computer vision problems. There the research is aimed at hypothesizing human perception based on Gestalt psychology (and here's the kicker) eventually leading to machines with perception. While working with psychologists in neuroscience like Kim the results should eventually lead to interpretations of human behavior for clinical purposes. Both these objective functions have quite different properties!

Most of my palpable research experience has been in coming up with heuristics motivated by Gestalt principles and apply blackbox methods from simulation based statistics, specifically particle filters for perceptual grouping and robot mapping problems. More lately I have been working with passionate young Assistant Professor,Vikas Singh whose interests are actually in applying and analyzing techniques from optimization theory and machine learning. This is opening up a lot of opportunities for me to actually start think and work on actually analyzing the efficiency/complexity of heuristics. I am seriously hoping to build some skills in "smoothed analysis". Then I need to be able to switch gears from thinking like complexity analyst, to psychologists, to being software engineer (one of my key skill-strengths). Anyways I will blog more specifics on that when I have some real progress in that line. Without further wrapping I will present what I originally intended to present that is a simple demo script to read output from DTI_TK in MATLAB.

You can download the package from here and run demo.m. I am not explaining the details because what I am offering is possible grease into the gear of DTI processing (to save some annoyance) not building the gear. The actual gear itself can be built pretty nicely using the documentation on the DTI_TK website itself.