[pymvpa] atlas coordinate system

[Yaroslav Halchenko]

Hi Lisa,

wow -- you found a hidden undocumented treasure...

The issue in your case is that atlases are loaded at maximal available
resolution ... ie in this case, it was 1mm, hence voxel querying provides your
output for a voxel at 1mm resolution, not 2mm like you've assumed I guess.

In [103]: print atlas._resolution
1.0

In [104]: atlas = Atlas(name="HarvardOxford-Cortical", resolution=2.0)

In [105]: atlas.labelVoxel([28,82,55],0)
Out[105]: 
{'labels': [[{'index': 0, 'label': 'Frontal Pole', 'prob': 50},
             {'index': 3, 'label': 'Middle Frontal Gyrus', 'prob': 23},
	         {'index': 2, 'label': 'Superior Frontal Gyrus', 'prob': 2}]],
'voxel_queried': [28, 82, 55]}


but once again -- all atlas handling is yet to be properly documented and
exposed.  It is great if it already works for you, but be careful and verify
the output (like you have already done ;))


On Tue, 23 Feb 2010, Lisa S wrote:
> I was hoping to use the atlas voxel labeler functionality in
> mvpa.atlases. I installed lxml, imported mvpa.atlases, and loaded
> FSL's Harvard Oxford Cortical Atlas using atlas =
> Atlas("HarvardOxford-Cortical.xml").

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