Usage: @ElectroGrid <[-strip Nx] | [-grid Nx Ny]>
[-prefix PREFIX] [-coords XYZ.1D] [-echo]
Creates a mesh representation of an electrode grid for use with SUMA
Mandatory parameters:
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
Optional parameters:
- -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 anatomical space.
[-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
-coords HPelectrodes_AF.1D’[0,1,2]’ 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
- -coords HPelectrodes_Grid.1D’[0,1,2]’
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 echo “
<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 (saadz@mail.nih.gov) SSCC/NIMH/ National Institutes of Health, Bethesda Maryland