[Simnibs-discuss] Define coil orientation in Localite

[Kristoffer Madsen]

The affine matrix indicates the transformation done to the coil coordinate
system in order to place it in the right position, hence the first 3
elements of the last column indicates the coil center position (typically
the location of the coil surface with highest A field) in the coordinate
system of the head model - so as you say.
The rotation is then given by the initial three elements of each of the
first three columns being unit vectors indicating x, y and z directions of
the coil in subject space.
If you want to express that in terms of angles you will have to decompose
into these - see for example:
https://people.cs.clemson.edu/~dhouse/courses/401/notes/affines-matrices.pdf
.
Best,
Kristoffer

Hello,

I am trying to optimize coil positioning and orientation for TMS but I am
not sure how to apply the affine transformation matrix in Localite
(matrix shown below). I used headreco to generate the headmodel.
- Because I used headreco, the values in the matrix are in native space, is
that correct?
- How do I define the entry target in Localite? Would this be 84.3, -8.4,
35.6?
- How do I calculate the rotation angle from this matrix? I am aware of the
coil and axes orientations in SimNIBS and Localite (attached) but do not
know how to use that information to set the rotation angle.

Affine matrix after TMSoptimize:
[[-5.7218e-03 -3.2704e-01 -9.4499e-01  8.4300e+01]
 [-8.5258e-01 -4.9224e-01  1.7551e-01 -8.3755e+00]
 [-5.2256e-01  8.0669e-01 -2.7601e-01  3.5573e+01]
 [ 0.0000e+00  0.0000e+00  0.0000e+00  1.0000e+00]]

Thank you in advance, I appreciate all the help I can get.
Goi Khia

--
Goi Khia Eng
Postdoctoral Fellow, Department of Psychiatry
New York University School of Medicine
Visiting Scientist
Nathan Kline Institute for Psychiatric Research
goikhia.eng at nyulangone.org
goikhia.eng at nki.rfmh.org


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