Monthly Archives: May 2012

The immediate and wide-ranging power of Twitter – discussion with Vaughn Bell and others on fMRI

I’ve only started using Twitter reasonably recently, but I’m finding that it’s very quickly become a near-essential part of my daily online routine, and I’d urge anyone who has a modicum of curiosity to give it a serious try. The ability to connect nigh-instantly to people around the world who share similar interests and occupations is incredible, and the 140-character limit is rarely too limiting once you get used to it. In fact, I’m constantly amazed at the high level of discussion which can be conducted within such a constraint.

As an example, this weekend there was an article in the Observer on fMRI by Vaughan Bell of Mindhacks fame. As i blearily groped my way through my regular Sunday morning routine of a cup of tea followed by several espressos, I was also engaged in an interesting debate about the article with the author (@vaughnbell), Chris Chambers (@chrisdc77), Tom Hartley (@tom_hartley), David Dobbs (@David_Dobbs) and a few others. The discussion was very kindly storify-ed for posterity by @creiner, and you can read it here.

I can’t think of any other way in which this discussion could have happened. I’ve never met Vaughn, or any of the other participants for that matter, and would have no direct way of contacting him/them otherwise. The great power of twitter (for me, anyway) is enabling groups of specialists like this to discuss in a public forum where anyone can chip in. If you’ve been on the fence about Twitter for a while, I urge you to give it a try – the more people who are active users, the richer the discussions will be!

TTFN.

PS. More additional thoughts on the original article can also be found on this blogpost.

UPDATE:
PPS. Tom Hartley has also just posted up a fantastic discussion related to the same issues on his blog too.

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A recreation of the world’s first neuroimaging experiment – LIVE!

A break from normal service today, as I thought I’d post up a little video of me being silly on stage on the occasion of Science Showoff  a few weeks ago. Science Showoff is a fantastic open-mic night for science communication, organised by the inimitable Steve Cross of UCL. People get up on stage in the back room of a pub in Clerkenwell, and do science-y things for the amusement (and occasionally even for the education) of the crowd.

For their May event, I thought I’d have a go at re-creating the world’s first brain-imaging experiment, live, on-stage, using nothing more than a table, a rolling-pin, and a kitchen scale. How was such a feat accomplished (I hear you gasp, dear reader, in tones hushed with reverential awe)? I shall explain.

Angelo Mosso – 19th Century Italian physiologist and ‘world’s first neuroimager’.

What’s often called ‘the world’s first neuroimaging experiment’ was conducted by a gentleman by the name of Angelo Mosso in the late 19th Century; a professor of physiology at the University of Turin. He’s generally credited with the notion that blood flow in the brain is related to mental activity; he arrived at this conclusion by studying patients with open head wounds – the pulsations of their dura would increase in frequency when the patients became agitated or engaged in some demanding mental task.

He also (apparently) designed an experiment in order to see the effect of increased blood flow during mental activity in ‘normal’, uninjured people. This was the first time an external apparatus had been used to visualise the internal processes of the brain – hence ‘world’s first neuroimaging experiment’. I say ‘apparently’ because the only write-up we have about the experiment is from William James’ journal of 1890:

“The subject to be observed lay on a delicately balanced table which could tip downwards either at the head or the foot if the weight of either end were increased. The moment emotional or intellectual activity began in the subject, down went the balance at the head-end, in consequence of the redistribution of blood in his system…”

Now, most people who’ve written about this experiment since, have generally cast doubt on the idea that this could ever actually work. But, being on occasion an incautious type, and thinking that even if it didn’t work it could at least be amusing, I figured I’d just give it a try. I used a couple of modern-day modifications – I got a cheap digital scale off Amazon, which could distinguish increments of 0.1g, and used a webcam pointed at the scale’s readout to display it to the crowd via a projector. I rested the head-end of the balance-board on the scale, and figured that any increase in blood-flow to the brain should result in an increase in weight on the scale. The able and moderately-willing volunteer for the experiment was my good friend Thom Scott-Phillips of Edinburgh (and Durham) University and the video was shot by Rita Santos. Unfortunately it’s impossible to make out the scale readout on the video, but it definitely worked. Oh yes. Absolutely. *Ahem*. I’m also slightly embarrassed to admit that it contains quite a few of the naughty swears, but, y’know, it’s just that kind of event. If it’s alright for Ben Goldacre, then it’s alright for me, dammit.

Without further ado then – the video (watch it on YouTube for glorious 720p):

Enjoy! TTFN.

iPad app for generating visual psychophysics stimuli

I’ve been meaning to write a new post which would be an update to my previous one on good psychology-related iPhone/iPad apps for a while now, but I just came across one app which is just too good not to share immediately. It’s a free app called RFSpotter, written by Nicolas Cottaris of the  IRCS and Dept. of Psychology at The University of Pennsylvania, and it generates simple visual psychophysics stimuli for use in mapping receptive fields and the tuning properties thereof. It has a very slick interface, where stimulus size, position and rotation can all be controlled by the usual iOS finger-gestures (e.g. pinch-to-zoom to change stimulus size, two-finger rotation for orientation) with many other parameters editable through a pop-up menu. It will do gratings, patches, dot-clouds, coloured stimuli – all kinds of things! Very, very neat indeed.

See this page for more details and a video of it in action, and visit the iTunes store here to download it.

Some screenshots:

The iPad really has the potential to be a serious platform for research, and it’s tools like this that will make it possible to do some really interesting work with it – here’s hoping we see many more specialist, research-oriented apps like this in the future!

PlagTracker – free online service for plagiarism checking

Just a very quick post to point you towards something I recently came across through the power of Twitterplagtracker.com. This is an online service which will scan a block of text (i.e. an essay/paper) and compare it to internet pages and a database of academic papers. The best thing about it though, is that it’s completely free!

I tested it out by pasting in a block of text from a previous post on this blog, and it seemed to perform pretty well, in that it correctly identified the source of the material as this site. It produces quite a nicely formatted report with links to the source material too:

PlagTracker.com report.

Pretty cool. The web interface means it probably isn’t that useful for essay-markers who want to batch-check a whole load of student essays, but if I was a student, I would definitely be using this service to check my essays before submission – plagiarism can happen by accident after all, and can often be fixed by just citing the correct sources. I say ‘often’ because you still have to remember the golden rule of undergraduate essays – for the love of God, don’t cite Wikipedia as a source!

TTFN.

Link-posting frenzy

There’s been a load of stuff I’ve been collecting for a while and been meaning to do write-ups of, but I’ve had a four-armed, wall-eyed gorgon’s arse of a week (got my SFN abstract in though – boo-yah) so I thought I’d just post them all up here with some minimal comments and let any interested readers pick through them at their leisure.

First up, a nice little proof-of-concept study which discusses the viability of using Smartphones in cognitive science research: Smart Phone, Smart Science.  This is from the same people behind the ScienceXL project.

A brief New York Times article on the development of computer algorithms for analysing natural language for various purposes, notably to detect lies.

Following on from my previous post on how to make a response box yourself for about £10, here’s how to make your own eye-movement recording headset for £30. This is pretty awesome.

The NeuroDebian home-page – this is a Linux distribution which contains a massive list of neuroscience-related software tools, including SPM, FSL, Freesurfer, python and loads of others. It’s basically an entire operating system optimised for neuroscience research. I’m not (currently) much of a Linux user, but if I was, this is what I’d be using.

Article on the Tech industry’s relationship with psychological disorders, including depression, suicide and Asperger’s.

HackCollege.com – A really good site for students, mostly geared towards a US audience. Lots of articles on general college-related topics but quite a few good tech articles too. Recent good articles on: doing presentations, blocking time-wasting websites, why Android is better than iOS for students (most obvious answer – it’s cheaper), and how to write without distractions.

StatsRef.com – a frighteningly comprehensive online statistics resource. Basically a free online statistics textbook. Also, in a similar vein, Prof. Andy Field’s Statistics Hell website. Almost as comprehensive, and definitely more amusing.

An interesting project called ProtoGenie – a web-based authoring toolkit for design and running of online experiments and data collection.

And finally, an interesting write-up of a study at the University of Illnois about students, ermmm… study habits. In a nutshell – over-reliance on Google, lack of knowledge about more advanced searching tools and specialist online databases. They should have read my earlier post about how to do research on the internet.

That should keep you going for a while, hmmm? TTFN.

More on response hardware: parallel port and USB.

I received a couple of e-mails this week from the inimitable, the mighty, the intrepid Prof. Chris Rorden, related to one of my earlier posts about parallel port response boxes. This pleased me greatly a) because he sent me a butt-load of really great information and links that I hadn’t been aware of, and b) because it’s exactly the kind of interaction with researchers that I was hoping that this blog would initiate.

Anyway, he pointed out a lot of new information. First of all, the paper that I cited from 2007 was essentially a re-tread of an older paper from 1992 which also has some nice circuit diagrams in, as well as some useful Turbo Pascal code (does anyone use Turbo Pascal anymore? I guess someone must…). He also directed me to this page which has a lot of information and circuit diagrams for experimental control of a PC.

Another hint he passed on was that on some computers the D0-D7 pins on the parallel port are not bidirectional – so may not work well for some applications, but the C0-C3 pins apparently always work for this kind of application (bottom right in the diagram below).

Parallel port pin diagram showing the three registers (data, status and control) and the ground pins (in green)

Regarding using USB input – he pointed me to this fascinating paper (PDF here) which has some theoretical analyses related to the relationship between true and measured RT, with limited resolution clocks. The surprising conclusion is that even with a clock with only a 30ms resolution, the effect on measured RT is negligible. This means that the 125Hz/8ms default USB-polling rate might not be such a big problem after all. Of course one should still be very careful about using ‘standard’ USB devices (i.e. keyboards, mice) for response timing as they can introduce significant errors as well.

Most interestingly, he pointed me towards a really sexy little device board from a company called U-HID.

The U-HID board – takes an input and transforms it into any kind of ‘standard’ computer input (key press, mouse-click, game-pad button – whatever!). Awesome.

What this does, in Chris’ words is:

“This allows 8 digital inputs to be read through the USB port. What is great is that it comes with software that allows you to assign any input to any keyboard or mouse button. The included software allows you to flash these changes to the device, so afterwards any computer will see the mappings you assigned. By default, this has a pretty good polling rate of 5ms.”

So, you can attach any kind of switch or input on one end, and when that switch is closed, the computer will see it as a key-press, a mouse-click, or whatever else you assign to it. The ‘Nano’ version of the board is really tiny, and is available from this site for only $35! This looks to be an incredibly useful bit of kit, and is probably the best solution I’ve seen for hooking up arbitrary devices to a USB input – really cool. Chris mentioned that he uses these boards for collecting responses in experiments, and also for reading the optical triggers from a Siemens Trio MRI scanner with his EZlog software (described here).

So – fantastically useful information – many thanks Chris! I’m a fan of keeping things simple, and parallel port inputs for collecting reaction times are certainly a good and easy solution; unfortunately parallel ports are largely obsolete these days, and most new computers don’t have them. The cards are still available for desktops, but in a few years these simple in-out ports may be completely unavailable. We’ll all have to move to USB devices at some point, and the U-HID boards are definitely the best-looking (and cheapest!) solution I’ve seen. I am definitely going to order a couple to try out.

Anyone else have any experience with the U-HID boards? Let me know in the comments. TTFN.