[Mne_analysis] hacking mne_setup_source_space

[David I Leitman]

Hi Eric,
 please see below:
On Apr 12, 2014, at 7:23 PM, Eric Larson wrote:

> It sounds like your definition of tris might omit some of the included vertices, in other words it's an invalid triangulation of the surface. IIRC the patch statistics are derived using the connectivity of the surface, which in turn is derived from the triangulation.
> 
> An alternative approach (and probably more future compatible) would be to make it so you're source space had three or more parts: the standard two hemispheres, plus an arbitrary volumetric grid or even surface, if you wish. There is some primitive and lightly tested support for this in mne-python, and some work on this might be done this summer. If you're interested, feel free to open an issue there and we can work on it.
> 
> 
Hi were could i find these primitive versions and support ?
> Another option that might work would be to not compute patch stats (no -cps), but I would guess faking the surfaces this way will cause (more) problems as you go, as various pieces of software may reasonably (but incorrectly) assume hemispheres refer to the original freesufer surfaces.
> 
> 
This is exactly what we did  we have been able create and add surfaces using some scripts from A.M winkler  at http://brainder.org with these and opiting --cps from setup source space we have been able to  apply the inverse model and get MNE estimates from amygdala and hippocampus.  At this point I am writing a script to automate the surface merge and create label files for the new merged surface and its sub cortical constituents. By merging in a specific order we are able to keep track of the vertices, such that each surface whit AMY and HIP have vertex numbers that are in a distinct range based on their merge order.
once the script is complete I will send it on to you and the listserve.

You mention problems down the road, what kind of problems do you think we might encounter?
> Eric
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David I. Leitman PhD

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