[Neuroimaging] Tracking from surface files

Bago mrbago at gmail.com
Fri Aug 26 21:31:03 EDT 2016

Hi all,
  I believe both of Ariels suggestions are good. Using the mesh vertices as
indices should be pretty clean, but sampling points on the mesh will allow
you to more finely control the density and number of seeds. I thing worth
mentioning is that fiber tracking works best when the seeds are in the
white matter tissues, so projecting 1 - 2mm from the mesh into the white
matter (when the mesh is along a white/gray boundary) might make the final
tacks better.


On Fri, Aug 26, 2016 at 4:21 PM Ariel Rokem <arokem at gmail.com> wrote:

> 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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