Understood, you have a vtkImageData (.vti or nii) AND a vtkPolyData (.vtp or vtk). That’s what I was missing.
You should be able to do the same in VTK.js.
To replace vtkProbeFilter, you can simply create a point data array (where a scalar is associated at each point), and you manually browse each point (xyz coordinate), convert the coordinate into ijk (i = (x - origin[0]) / scaling[0], j = (y - origin[1]) / scaling[1]…) and get the voxel value at this local coordinate.