brain browser?

August 13, 2008 8:48 AM

Neuroanatomy filter: is there PC software to visualize in 3D the different anatomic parts of the brain (with labels) and maybe even their interconnections (tracts)?
posted by bbranden1 to science & nature (10 comments total)

have a look at the harvard whole brain atlas
posted by paradroid at 9:39 AM on August 13, 2008

Thanks, looks like a good site, paradroid. I should have been clearer: I'd like to be able to isolate anatomic structures and move them around in 3D to get a better sense of how they relate anatomically and neurologically to the brain as a whole.
posted by bbranden1 at 10:01 AM on August 13, 2008

I'm not sure if you can get isolated representations of particular structures, but you can definitely get rotatable 3D brains with MRIcro. You can also highlight regions of interest or neuroanatomical structures on the rotatable brain.
posted by solipsophistocracy at 10:06 AM on August 13, 2008

There's nothing that I've seen that is great at this (neuro grad student here), but brainmaps.org is decent and free. Haven't checked them out in a while so see if their download section has anything that fits the bill.
posted by neuroking at 10:17 AM on August 13, 2008

You can try the Brain Atlas dataset at Harvard's Neuroimage Analysis Center. You'll have to download Slicer 3 and probably read the dataset tutorial, but it gives you a 3D atlas of the brain. The rendering is all isosurfaces, so there can be a lot of improvements. It does offer some white matter tracts though.
posted by demiurge at 11:13 AM on August 13, 2008

You might give the BrainVoyager Brain Tutor a try. It uses the same graphical engine as BrainVoyager software suite, which means you can get a wonderful 3D representation of the cortical surface to explore. It is a free download, so the price is right, and it is easy enough to use that middle school students can use it.
posted by prefrontal at 11:45 AM on August 13, 2008 [1 favorite has favorites]

These are terrific answers. Keep them coming!
posted by bbranden1 at 11:50 AM on August 13, 2008

Seconding the Harvard SPL atlas that demiurge pointed out. Also, I don't know how Slicer3 is now, but last year it was very buggy. Slicer2 takes some getting used to but its not bad at all. I found MRIcro rather painful to use.

We used BrainStorm in a first-year neuroanatomy course, and it was alright. I found a book-format atlas was far more useful, since you go through slice by slice. This is especially important for brainstem nuclei, since they come & go at very specific points.
posted by devilsbrigade at 1:11 PM on August 13, 2008

Hm, actually, BrainStorm appears to be the slices one. There was another Java one that we used too, which I can't find now.. I'll get back to you if I remember it.
posted by devilsbrigade at 1:17 PM on August 13, 2008

Hi,
I am producing a 3D interactive brain that requires no downloads and works in Flash. You can view a demo at our G2C Online site (G2C stands for Genes to Cognition. Choose the 3D brain from the menu.
The full brain will be live on or before November 14th (2008).
posted by joconnol at 1:39 PM on October 27, 2008