[pymvpa] digging for "the hidden treasure" - the PyMVPA atlas module

[Michael Hanke]

On Sun, Feb 27, 2011 at 11:25:58PM +0100, Susanne Greiner wrote:
> The other day I came across the PyMVPA atlas module (which
> unfortunately is not yet documented). Looks like that could
> definitely simplify life in this kind of case. For example once you
> have loaded an atlas, there is the function label_voxel// which does
> all the looking up for you:

This was never added properly to PyMVPA, because we were never sure
whether it would be the best place to put it. I guess the undocumented
stage was more or less intended to keep people from using it ;-)

> So is anybody of you already using the atlas module a lot and can
> give me a hand with the following example:
> - To label: searchlight results in subject space, lets call that
> dataset sl_map
> - Preferably using Talairach (not my choice) from FSL
> - the coordinate system of the atlas modul [26,26,26] would
> correspond to the sl_map.fa.voxel_indices!?
> - what exactly does this levels option do?
> - the other way round should be possible using the find option!? I
> tried searching for "Cortex", but as soon as there are multiple
> matches the option finishes in an error...

I leave the answers to this one to Yarik, as he wrote it back then. But
I want to mention PyROI, which seems to address some of the issues (and
is documented) -- although the focus is a bit different.

  http://web.mit.edu/mwaskom/pyroi/

Michael

-- 
Michael Hanke
http://mih.voxindeserto.de