Initiate simulink model with data depending on Simulink variables

I would like to run a Matlab script to iniate my Simulink model. Now i am using "InitFcn Callback: Load_profiles_script3.m" which in itself works fine. However I would like to be able to set some parameters in Simulink which are used by the Matlab script. Another way I tried is using the Matlab function block. However the Matlab script contains some functions not supported by Simulink and therefore this is not possible. So my question is, can I somehow first run a part of my Simulink script (define a few parameters) , then run a Matlab script outside simulink using these parameters and then run the rest of the model?