Monday, 14 November 2011

Modern War-fMRI : Graphics Cards for Science

Videogames and neuroscience have a rocky relationship.

On the one hand you have Susan Greenfield and her games-hurt-the-brain theory. But she's not representative of neuroscientists as a whole: games have also helped neuroscience, for example, in this study of the neural correlates of "flow" experiences.

Now neuroscientists have another reason to be thankful for games, according to a new paper. It turns out that modern 3D graphics cards - which mostly exist in order to render videogame visuals - can be used to do fMRI data analysis.

According to Sweden's Eklund et al, a graphics card can perform intensive fMRI analysis hundreds of times faster than a regular processor of the equivalent speed, because graphics processors make use of parallel computing optimized for 3D images and that's ultimately what all brain scans are.

They developed a way to run non-parametric statistical analyses of brain imaging data. Proponents say that non-parametric stats have many advantages over conventional parametric ones - and they're certainly becoming increasingly popular. But they involve doing far more calculations. Thousands of times more, in some cases.

It turns out though that armed with 2.5 GHz CPU and three NVidia GTX 480s, and making use of NVidia's graphics programming language, they were able to cut the time to analyse one person's brain with 100,000 permutations, from 24 hrs to just 9 minutes. The whole setup cost $4000, so it's not cheap, but they say it's "a fraction of the price for a PC cluster with equivalent computational performance" i.e. one relying on lots of general purpose processors, rather than graphics cards. Even on GTX480 did the job very well.

Best of all, this gives neuroscientists an excuse to spend their grant money on awesome gaming rigs. Why do I want the latest GForce on my work computer? To do non-parametric data analysis, obviously. Sure, it would also allow me to run Modern Warfare 3 at the highest settings... but that's not why I want it.

ResearchBlogging.orgEklund A, Andersson M, Knutsson H (2011). Fast random permutation tests enable objective evaluation of methods for single-subject FMRI analysis. International journal of biomedical imaging, 2011 PMID: 22046176

26 comments:

Anonymous said...

Simulated (and especially real) violence is a waste of consciousness.

Anonymous said...

"It turns out though that armed with 2.5 GHz CPU and three NVidia GTX 480s, and making use of NVidia's graphics programming language, they were able to cut the time to analyse one person's brain from... down to just..."

From what to what???? I want to know!

Anonymous said...

@Stephen your post is a waste of consciousness.

@Anon Im curious too

Richard said...

Anonymous 1 & 2: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199190/table/tab2/ is a speed increase table in the paper.

GPU computing is really gaining some momentum in neuroscience it seems, especially now the Matlab parallel toolbox allows you to take advantage of your GPU without you having to know how to code for your GPU specifically, and PyCUDA provides a nice Python wrapper around the CUDA C code. I've recently been using the nice Brian ( www.briansimulator.org ) model fitting toolbox and get a speed increase of 2 orders of magnitude on my GeForce GTX 275 over my Core i7 CPU. The architecture of a GPU makes it particularly suited to "embarrassingly parallel" problems, where the problem can be split into many smaller problems that are independent and can be worked on concurrently.

Neuroskeptic said...

Woops, well spotted.

Ivana Fulli MD said...

Anonymous14/11/11 22:47 wrote:

"@Stephen your post is a waste of consciousness."

Stephen Crowley dared to write out of protection of a boring and hyperprotective anonymous pseudo like "Anonymous":

"Simulated (and especially real) violence is a waste of consciousness."

First, I want to thank Stephen for an interesting opinion I didn't know about and would be glad of some explanations about it since I have not a clue about what that means for him.

Second, I strongly doubt that the brave Anonymous 14/11/11 22:47 isn't being intolerant to a criticism of something he enjoys.

Of course I cannot rule out that Anonymous 14/11/11 22:47he might have understand Stephen's critics of violent videogames better than I do but it is no excuse since he insulted a person without giving arguments.

Ivana Fulli MD said...

I am waiting with genuine interest for Stephen Crowley to explain himself more.

On another point of neuroskeptic's post:

Many military technology advances and innovations have been used afterwards with the greatest of benefits for civilian activities.

It doesn't means that the same amount of money and researchers ' intelectual ressources would not have had the same results in advancing technology -look at Bill Gates's foundation advances toward a malaria vaccin.

Neuroskeptic said...

I dunno Steven. Real violence is bad but there's nothing wrong with pwning noobs on Modern Warfare, in moderation.

Anonymous said...

As somebody that has written device drivers for graphics cards and has long known their potential for fast desktop computing I have this to say about video games: They are a huge waste of time and I have no doubt that there is a causal link with video game use and childhood obesity. These are not just games.

Neuroskeptic said...

Sure they're a waste of time. Isn't that the point of all entertainment? It wastes time in a pleasant way.

Ivana Fulli MD said...

Aren't not anymore children supposed to learn pleasantly a lot of skills and increase a lot of their abilities (social, intellectual and fitness abilities) having fun through playing on the playground or playing at home and singing and the like?

May be adults only ought to be allowed to decide for themselves how long they can spend playing with videogames like how many beers they can drink.

Anonymous said...

Neuroskeptic wrote:

"It wastes time in a pleasant way."

Obesity and Type II Diabetes are not pleasant.

omg said...

You can't get fat from eating video games you noob.

Vince said...

Following up on what Richard said, mainstream adoption of GPGPU has really started to take off; which is fantastic given the excellent mapping between the massively parallel architecture of GPUs whereby they hide latency by keeping hundreds or thousands of threads in flight and most imaging and neuroscience data which is parallel and independent.

Note the perfectly linear performance scaling from one GTX480 to three!

Vince said...

Also, concerning the cost: If it's not financially viable or necessary to build your own rig -- maybe you're just doing a short-term trial, or you can not predict the computational ceiling -- you can rent time on Amazon's EC2 clusters that use the same nVidia Tesla GPUs.

http://aws.amazon.com/hpc-applications/

Ivana Fulli said...

omg

"You can't get fat from eating video games you noob."

You crook! I bet you wrote that sentence without any personal or bibliographic experience of actually eating video game!

And eating when playing video game can be very uncarefuil and unhealthy plus the sedentarity.

Ivana Fulli said...

Neuroskeptic
@ NS 15 November 2011 17:59


I promise not to intervene and bore your readers for at least 15 days if you explain to me yor understanding about wht Stephen meant by "waste of conciousness.

I saw he practise Yoga and it can be a Californian concept or even a more eastern ne or my lack of grasp of the English language.

I am interested because, sadly, my perspective is that there is no easy answers about the overall benefit of playing video games.

I am sure that you are pessimistic though and some people - I am sure - get more out of playing video games than you think ( reduction of time of reaction for example useful to drive a car or realization that drinking alcohol might impair performances etc).

I would advise any surgeons to play if they are concerned about operating with the minimum cut of skin of their patients.

Idem for the dangers: individuality mkes some people at risk of addiction or obesity but some teenagers play a lot without being addict and losing grades at school nor sex-appeal and social restraint.

Richard said...

@Vince good point re: Amazon cloud, though a suitable GPU can be had for ~£150, which is another nice thing about using GPUs. Plus then you can pwn n00bs Modern Warfare 3 with top graphics settings (though sadly I tend to be the n00b getting pwned...)

Ivana Fulli MD said...

The Research Autism Lorna Wing

series of conferences and seminars present:



Computers and Autism –

A Blessing or a Curse?



Date: Thursday 24 November 2011

Venue: Church House Conference Centre, Westminster, London

See my point and why any honest original thinking is needed?

omg said...

Ivana, noob, overall weirdo, I eat bananas when I play Donkey Kong, mushrooms with Mario.. you know the game that goes dudududii nerdududu nohohoho life.

You, Crowley and Susan Greenfield + noobs should salute to the sun pilate your way through the war against terrorism, fight poverty, democracy, protest.

Simulated environments are a neccessity in most elite professions. Just because they've commercialized what sells, don't mean it can't be consumed in moderation.

skm said...

You don't need to get a dedicated console for it, you might be able to use your current laptop. I am not telling your boss though.

If you do end up playing around with graphics cards for neuroscience things, I'd love to see your posts on the process.

and hordes of programmers would come to your aid if you get stuck along the way.

Ivana Fulli MD said...

omg16 November 2011 16:57

First, what I think of that British journalists icon of neurophysiology is that even british journalism had ceased to be great and that it is a pity.

Second,facts prove difficult for you to find somebody more different from that childless successful academic than I.

I had been like her a young beautiful (beautiful for an oxford research registrar in a psychopharmacology dept that is) and bright young woman aspirant to a neuoscientis career.

At the same time we both have been blessed with an Oxford education although mine was much shorter than hers (6 months experience of research registrar in the Oxford psychopharmacology unit of Pr Gelder).

After that we could not be more different in our choices as human beings and aspirant scientists.

I published young in Psychological Medecine (no merit of mine all of Pr Gelder and Phil Cohen).

After that I came back to France and ruined any prospect of an academic career in France.

Not because I had an idea of research but because I refused to give it up before published in The lancet in 1986.


A modest project with only qualitative data that went to be published as an article in The Lancet in 1986 because it was original.

I dared to make a point in favor of an action of sexual female steroid on the brain

It challenged a psychonanalyst psychodynamic way of thinking.

Not because we were 10 years before it was shown that the receptors existed indeed for female steroids in the brain.

This point just made me to accept an intelectual robberry of my property of the study I conceived alone but thanks to my stay in Oxford.

I had to fight for my name in fourth position after the name of a gastroenterologist pretended statitician for doing a X2 analysis!

This is just plain academic career stupid in any country.Hardly somthing your british icon of female in the sciences world would have done, would she?

Plus, I even stop to earn money doing only pro bono work in an informal manner in order to home school properly two very bright children.

The French school system refused to acknowledge that they were too bright for the curiculum for them to behave and not be bullied.
They were accused of lack of repect of their school duties and even of a the teacher of math I was told. The on eaccused of lack of respezct of a math school teacher answer that that man didn't teach much math and was not bright.It is certain that one got a broken arm after a vicous attack during a gym class.

With the help and complicity of school physicians with a s and social workers they were accused of being intelectually limited.

Both are PhD candidate and have a spectacular curriculum so far.


But I was accused of being crazy and dangerous for my sons and threatened of going to jail in writing if I continue to homeschooled them in 2002.

At that moment I issue a videogames prohibition for more than given hours some days of the week follow by a complete prohibition : it was mandatory for my sons to excel and get as quickly as possible their high school diploma with honors.

Both got the more difficult highscholl diploma (math major) two years in advance and with honors (facts and no corelation with the previous paragraph) .

Ivana Fulli MD said...

omg 16 November 2011 16:57
wrote against my poor self 3 very manly -not gentelmanly at all- angry paragraphs.

I really do not care about that egocentric (he obviously read only what I wrote in answer to his funny enough line)angry young man.

I wouldn't treat him unless it were to be an emergency and no other psychiatrists were available in a reasonable time.

I already agree with his writing of a possible safe and reasonnable use of videogames and the usefulness for some technical top professions like pilots and surgeons (IF 15 November 2011 22:04-If 16 November 2011 12:24)

I want to emphazize that:

Neither omg nor I nor anybody can tell today that it has been scientifically established that it is possible for anybody to play video game safely ( no diminution of fitness and moral values and no more depression or hallucination etc...) and not becoming addicted.

Studies are needed on the subjects with bright and broad minded enough scientists.

What I can bet is that this answers is probably subtle and gray not taking into account frauds and the higher risk of bias with a young generation of scientists often themselves great videogames players.

Placid Way said...

eventually that is been accepted that at some how gaming technologies are beneficial and helpful to medical. Doctors in Turkey gaming stuff as affects the brain, so also does give some thing as well for betterment.

ivana Fulli MD said...

Placid way

Unless you are the anesthetist or a Jehova witness speed is not the only quality you are looking for in a surgeon if you want to survive in the best possible condition.

Some studies show that surgeons practising video games get speed in the operating room with some procedures.

No counterintuitive results since surgeons can work not on the open air but through tubes introduced into the patient and producing images on a screen.

But just imagine -for the seek of discussion - that playing violent video games were to make surgeons less able to take the right important decisions or be too impulsive in desintegrating a little bit of a sane and still useful artery or whatever.

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