Dear Sanjiv,
you may set the apodization in the FBG Sensor component in OptiSystem to Uniform or Gaussian. However, you may use the OptiGrating FBG component in OptiSystem such that you design the grating in OptiGrating using any apodization, then load the transmission and reflection spectra in the component in OptiSystem and use it in your project. I am attaching two images to show the components in OptiSystem.
Regards,
Ahmad