AFNI program: @ElectroGrid
Output of -help
@ElectroGrid <[-strip Nx] | [-grid Nx Ny]>
[-prefix PREFIX] [-coords XYZ.1D]
Creates a mesh representation of an electrode grid for use with SUMA
One of the two options -strip or -grid
-strip Nx: Make an Nx strip (array) of electrodes.
-grid Nx Ny: Make an Nx by Ny grid of electrodes.
A node at (i,j) has a node ID = i+Nx*j with
0<=i<Nx and 0<=j<=Ny
-coords XYZ.1D: Specify the coordinates of the nodes on the grid,
or the array. XYZ.1D should have three columns,
with each row specifying the coordinates of one node.
You can use sub-brick selectors to select from more
than three columns.
The fist row is for node 0, second for node 1, etc.
The ordering is trivial for an array. For a grid you
need to be a bit more careful. You march along the x
direction first, then move up the y.
A flat grid (Z=0) for a 2x3 electrodes system would
have coordinates layed out as such:
# X Y Z (ID shown here for clarity)
0 0 0 0
1 0 0 1
0 1 0 2
1 1 0 3
0 2 0 4
1 2 0 5
Usually, you would have coordinates in the subject's
[-prefix PREFIX]: Use PREFIX for the output surface.
[-with_markers]: Add markers to the surface at each electrode. See
examples below for detail.
[-echo] : set echo
Make a flat 4 electrode array:
Node X coordinates are regularly spaced from 0 to 3.
Node Y coordinates are small and random, to allow array
representation as a surface
@ElectroGrid -prefix flat4 -strip 4
suma -i flat4.gii
Make a flat 4 electrode array and assign anatomical coordinates
in first three columns of file: HPelectrodes_AF.1D
@ElectroGrid -prefix HP_array -strip 4 \
suma -i HP_array.gii
Make a 2x3 flat grid:
Node coordinates are on a regular grid.
@ElectroGrid -prefix flat23 \
-grid 2 3
suma -i flat23.gii
Make an 8x8 grid, and assign to its nodes the coordinates listed
in the first three columns of HPelectrodes_Grid.1D
@ElectroGrid -prefix HP_grid \
-coords HPelectrodes_Grid.1D'[0,1,2]' \
-grid 8 8
suma -i HP_grid.gii
Say you're too lazy to know the grid (or strip) count
and you have a file with the electrode's coordinates.
@ElectroGrid -prefix HP_grid2 \
suma -i HP_grid2.gii
You can also give the grid a special appearance by adding
special node markers. For example, put the following text
in file marker.niml.do
<nido_head coord_type = 'mobile' /> \
<S rad = '2' style = 'silhouette' stacks = '20' slices = '20' /> \
" > marker.niml.do
Then create a spec file for one of the grid surfaces:
quickspec -spec grid.spec \
-tsnadm gii pial HP_grid2.gii y SAME marker.niml.do
suma -spec grid.spec
Using option -with_markers will do the trick for you.
Ziad Saad (firstname.lastname@example.org)
SSCC/NIMH/ National Institutes of Health, Bethesda Maryland
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Sun Mar 7 20:06:24 EST 2021