[pymvpa] atlas coordinate system

[Lisa S]

Thank you, that's exactly what I was missing :)

On Tue, Feb 23, 2010 at 2:30 PM, Yaroslav Halchenko
<debian at onerussian.com> wrote:
> 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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>
>
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