The really-very-excellent Ben Thomas (of The Connectome) recently posted something on facebook which got me thinking; it was a link to a project called NeuroSynth, which is an ongoing collaboration between several high-profile brain researchers and groups (details here) to provide an easy method for performing automated large-scale analyses (or meta-analyses) across a large portion of the neuroimaging literature. Briefly, the builders of this system have developed a way of automatically parsing the full text of published articles, and extracting 1) the parts of the brain which are active (as reported in the paper by a commonly-used 3-axis coordinate system) and 2) the topic of the paper (by looking at which terms are used with high frequency in the paper). Using these two bits of information, a huge meta-analysis is then conducted, and brain-maps showing areas which are reliably associated with particular terms in the literature can be produced. Wonderfully, they’ve made the brain maps available on the web, and you can even download these maps in the standard NIFTI (*.nii) format.
Give it a try with some common terms, e.g.:
Fun, huh? One of the best applications that immediately springs to mind when looking at these data is that these brain maps could be used to constrain the search-space in new brain-imaging experiments – for instance, by using these maps to define ROIs for hypothesis-driven analyses (something which I’m very keen on), or for defining regions for multi-voxel-pattern-analysis. Read the rest of this entry
A brief anecdote – last week I had to fix a website. Doesn’t matter which one, but there was a link that needed removing. Easy, you might think; not so, unfortunately. The link was embedded in a piece of malicious code in a website theme, which uses a bit of web technology called PHP. Now, I know very little about PHP, but I managed to find the right bit of code on the server and opened the file, to be greeted with absolute gibberish – a totally unintelligible string of numbers and letters. A bit of googling revealed that the code had been intentionally obfuscated by encoding it in base-64 - sneaky. A bit more googling eventually turned up a base-64 encoder/decoder which made sense of it, I stripped out the offending link, and uploaded a new version of the file back to the web server (using this awesome online ftp client), which (miraculously) worked! Job done.
The point of this anecdote is that you can achieve a lot with computers with a tiny bit of knowledge and a lot of experimentation – or just hacking around. Read the rest of this entry
I decided to put together a computer skills checklist. A lot of the things on this list are not specific to psychology and should be part of the training of every student. I would advise students to work through the list and note down any entries that you’re not comfortable with – finding out how to do these things and ticking off every item on the list will definitely advance your knowledge and help you out in future. Some of the things on the list have already been covered on this blog, and some I’m planning to cover in the future. Let me know in the comments if you think I’ve missed anything!
Green text denotes a basic/essential skill, orange means intermediate, red means it’s an advanced skill. Most students should be able to tick off all the green ones straight away – if you can’t you’ve got some work to do! Read the rest of this entry