Wetware software

One of the things that psychology/neuroscience students often find hardest is learning about brain anatomy. Most psychology courses nowadays have some neuroscience element to them, and for beginners unfamiliar nomenclature like ‘ventro-lateral prefrontal cortex’ and ‘rostroventral-medial medulla’ can be (rightly) terrifying. Further confusion can be caused by some papers referring to numbered Brodmann areas, and other papers preferring to use functional descriptions of brain areas, such as ‘motor cortex’ or ‘hMT/V5’. The primary visual cortex in the occipital lobe might be referred to functionally (V1), by Brodmann area  (17), anatomically (calcarine sulcus) or cytoarchitectonically (‘striate cortex’).

A lot of this confusion can be cleared up by a bit of basic reading. The wikipedia page on Anatomical Terms of Location is excellent, as is this very clear page specifically on anatomical terms used for the human brain. Brodmann areas are also explained here.

After ten years of reading papers and spending a large proportion of my everyday life looking at brains in various ways, my knowledge of neuroanatomy is still (and probably always will be) far from exhaustive. However, there are some websites and software that I use extensively for looking things up. The ‘gold standard’ for this kind of anatomical work is still to use a good-quality brain atlas (this one is a current favourite) but for a quick reference when I’m reading a paper and come across an unfamiliar term or need to know roughly where something is in the brain, the resources detailed below are perfectly good, and much more convenient.

First up is ‘BrainTutor’, which is produced by a very nice bunch of guys in the Netherlands (Brain Innovation Inc.), who also make software for analysis of fMRI/EEG/MEG data. BrainTutor is free, and cross-platform; you can download it here. Once you install it you are greeted with the main interface:

From here you can view the brain in either a 3D-modelled and rendered view (as above) or as orthogonal slices on a MRI image by selecting ‘Volume view’ at the top left. The 3D brain can be rotated, zoomed, and moved by various mouse/key combinations. Ctrl-clicking on part of the brain highlights that part, and (depending on what is selected on the toolbar at the top right) tags it with the relevant gyral/sulcal/Brodmann/functional label. Here I’ve selected ‘fMRI’ and highlighted the (functional) visual motion responsive area in the occipital lobe – hMT/V5. Brain regions can also be highlighted by clicking a term in the list on the left. Also provided is a brief description of each area’s location and function in the blue box on the right.

BrainTutor is great for learning about the brain, but it’s also incredibly useful in other ways. The 3D-rendered brain images are really beautiful, and, particularly if you have a large high-resolution monitor, can be used for creating great-looking figures using screen-grabs – I use it to make illustrations for a lot of my presentations and lectures. Brain Innovation even make a version for iOS devices (iPhone/iPod/iPad) which is great for looking things up in lectures, and for impressing your friends! If you have easily-impressed or particularly geeky friends, that is.

Another decent app for iOS which does similar things is ‘3D Brain’, available on the iTunes store here. This one seems a bit idiosyncratic in which areas it covers and defines, but it definitely has a lot of good information in it, and some nice transparent brain views and animations as well.

Another resource I often use is the online brain atlas produced by Harvard Medical School, available online here. This has a great deal of information about both the healthy and diseased brain, but the most useful resource is a java-based clickable brain atlas, which labels structures in pretty fine detail. This is not the most intuitive site though, so you might need to spend a bit of time familiarising yourself with the interface before you get much out of it. Another very cool online brain atlas is from Michigan State University and is available here. This one allows the user to choose from three orthogonal sections, and has clickable images which open larger versions, which then can display labels for all the structures visible in that slice – very useful.

A further amazing resource is brainmaps.org which claim to have over 60 terabytes of brain image data available online. They have brain images from lots of species (even some marsupials!) and images from lots of different datasets including (for humans) MRI images, post-mortem sliced images and sections stained in various ways.

Lastly, a slightly different kind of resource is the Brede Database here. This is a database of functional neuroimaging papers, and the coordinates in the brain that they ascribe to various functions. Searching for an anatomical or functional term (say ‘orbitofrontal cortex’ or ‘premotor cortex’) will bring up a list of papers which mention that term, and also a cartoon of the location in the brain. Not so great for learning about neuroanatomy, but invaluable if you have a piece to write on a particular brain area.

That’s all on the topic of software for neuro-nerds. If I come across anything else really great in the future I’ll try and remember to update this post!



About Matt Wall

I do brains. BRAINZZZZ.

Posted on December 1, 2010, in Software and tagged , , , , . Bookmark the permalink. Leave a comment.

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