[Neuroimaging] Tracking from surface files

[Ariel Rokem]

Hi Kristian,

On Fri, Aug 26, 2016 at 4:51 PM, Kristian M. Eschenburg <keschenb at uw.edu>
wrote:

> Hello
>
> I'm interested in tracking streamlines using a mesh like that included in
> the HCP files, instead voxels, as seed points. Does Dipy have this
> functionality?
>

Thanks for your email.

Seeds in dipy (e.g., inputs to the `LocalTracking` class ` __init__`
function; see example:
https://github.com/nipy/dipy/blob/master/doc/examples/introduction_to_basic_tracking.py#L98
) are an array of 3D coordinates, so they don't have to be voxels. But - I
don't think we don't have a utility function that does what
`seeds_from_mask` does, but for meshes (a seeds_from_mesh function).

Do the mesh files from HCP contain the 3D positions of the vertices? You
could potentially use the positions of the vertices as seeds. A more
sophisticated approach would sample the surface of the mesh between
vertices. But I haven't thought about this very deeply, and I'd be curious
to hear if others have thought about potential pitfalls with these
approaches. If you end up writing something along these lines (even just
sampling the vertices) consider contributing that alongside
seeds_from_mask!

Cheers,

Ariel


> Thanks!
>
>
> k
>
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