Hello,
You may be able to use wb_command to convert a list of surface coordinates into
a list of surface vertex indices. wb_command is included with Connectome
Workbench and must be run from within a terminal window (Command Prompt).
“wb_command -surface-closest-vertex” accepts as input a GIFTI surface file
and a text file containing XYZ coordinates. The output is a text file
containing the indices of the vertices nearest the coordinates. If you are
using MNI coordinates, the surface must be an anatomical surface that is in MNI
stereotaxic space.
Once you have a list of vertex indices, return to Connectome Workbench. Select
Window Menu->Identify. In the Identify Brainordinate Dialog, select Identify
Surface Vertex, choose the Structure (Cortex Left or Cortex Right), enter a
Vertex Index (from the output of wb_command -surface-closest-vertex), and press
the Apply Button. If there is connectivity data corresponding to the vertex,
connectivity data is loaded. Repeat for each vertex index.
Note that “wb_command -surface-vertex” finds the “closest vertex" and it may
be a long distance from the coordinate that you provide. Each time the Apply
button is clicked in the Identify Brainordinate Dialog, the Information Window
will contain the 3D coordinate corresponding to the vertex index and it should
be compared to the coordinate provided as input to “wb_command
-surface-vertex”. An identification symbol is also placed on the surface and
should be inspected to verify that it is the correct anatomical location.
wb_command -surface-closest-vertex
FIND CLOSEST SURFACE VERTEX TO COORDINATES
wb_command -surface-closest-vertex
<surface> - the surface to use
<coord-list-file> - text file with coordinates
<vertex-list-out> - output - the output text file with vertex numbers
For each coordinate XYZ triple, find the closest vertex in the surface,
and output its vertex number into a text file. The input file should
only use whitespace to separate coordinates (spaces, newlines, tabs), for
instance:
20 30 25
30 -20 10
John Harwell
On Aug 14, 2018, at 8:38 AM, Kwan-Jin Jung
<[email protected]<mailto:[email protected]>> wrote:
Hi,
Is there a way to define the seed location, i.e., MNI coordinate, on the cortex
in wb_view for the functional connectivity?
At this time, I input the coordinate into the Volume tab and I iteratively find
a similar coordinate on the surface.
But it is tedious and difficult.
<image001.png>
Kwan-Jin Jung, Ph.D.
UMASS Amherst
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