Re: [HCP-Users] Neighbors of a vertex

[Timothy Coalson]

Workbench does this internally, but it doesn't currently have a command to
output it (the number of neighbors varies per vertex, so it could be hard
to make efficient use of in something like matlab).  The .surf.gii file has
this information in it, in the triangles array, so if you load it, you just
have to build a lookup based on that.  Each triple in the triangles array
is the vertices of a single triangle.

When we use neighbor information (things like gradient, where it needs to
respond to as small a local neighborhood as possible), we also take the
length of each edge and/or coordinates of each neighbor into account, since
the triangles don't have to be close to equilateral.  If we are doing
something that uses larger spatial extent (smoothing), we instead use
geodesic distances rather than single-hop neighbors, so that we get
circular ROIs with distance information, regardless of the mesh topology.
This is exposed for a single vertex at a time via wb_command
-surface-geodesic-distance (the full matrix would be large and takes a
while to compute, but it can be added if it would be sufficiently useful).

Tim


On Wed, Feb 28, 2018 at 1:22 PM, Shankar Tumati 
wrote:

> Hello experts,
>
> I would like to get a list of neighbors of each vertex in a 32k surface
> file. How can I do this with workbench? If not with workbench, is there
> another way to get this info?
>
> Thank you.
>
> Best,
> Shankar
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> HCP-Users mailing list
> HCP-Users@humanconnectome.org
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>

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Re: [HCP-Users] Neighbors of a vertex

[Yaroslav Halchenko]

On Wed, 28 Feb 2018, Shankar Tumati wrote:

> Hello experts,

> I would like to get a list of neighbors of each vertex in a 32k surface file. 
> How can I do this with workbench? If not with workbench, is there another way 
> to get this info?

quick one:  we rely on neighborhood information in PyMVPA while 
doing surface-based or surface-guided (selects neighboring voxels)
searchlight in PyMVPA. See e.g.
http://www.pymvpa.org/generated/mvpa2.support.nibabel.surf.Surface.html?highlight=surface#mvpa2.support.nibabel.surf.Surface.neighbors
http://www.pymvpa.org/examples/searchlight_surf.html?highlight=surface

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik
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[HCP-Users] Neighbors of a vertex

[Shankar Tumati]

Hello experts,

I would like to get a list of neighbors of each vertex in a 32k surface file. 
How can I do this with workbench? If not with workbench, is there another way 
to get this info?

Thank you.

Best,
Shankar
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