FEM simulations

In NRV, FEM model are described in FEM_stimulation object. The object defines the shape of the nerve, the number of fascicles and their shapes, etc. If model_fname in the FEM_stimulation initialization parameter set to None, NRV will use Fenicsx to solve the FEM. Else, and if comsol is also True, Comsol will be used

Warning

Use FEM multiprocessing with caution. We recommend keeping Ncore to None for now.

If you want to use Comsol, you must provide a parametric comsol mph file. We currently provide three comsol template files:

Nerve_1_Fascicle_1_CUFF.mph which describes a monofascicular nerve wrapped with a monopolar cuff electrode
Nerve_1_Fascicle_1_LIFE.mph which describes a monofascicular nerve wrapped with a monopolar LIFE
Nerve_1_Fascicle_2_LIFE.mph which describes a monofascicular nerve wrapped with two monopolar LIFEs

Warning

Use of Comsol for FEM is not recommended. Support of this feature might be removed is future release.

Nerve and fascicle are parameterized, and their geometrical properties can be modified with the reshape_nerve() and reshape_fascicle() methods, respectively. The reshape_outerBox() can be used to set the size of the outer box.

Note

To add fascicle to the nerve, simply call the reshape_fascicle() method with a new ÌD:

my_FEM.reshape_fascicle(fascicle_d1, fascicle_y1, fascicle_z1, ID = 0) #create a new fascicle with ID 0
my_FEM.reshape_fascicle(fascicle_d2, fascicle_y2, fascicle_z2, ID = 1) #create a new fascicle with ID 1
my_FEM.reshape_fascicle(fascicle_d3, fascicle_y1, fascicle_z1, ID = 0) #change diameter of fascicle 0

Any electrode object can be added with the add_electrode() method. This method serves also the purpose to link a stimulus object to the model.

Warning

If the FEM_stimulation is based on a comsol template, only the number of fascicle and the electrode model specified in the template can be parameterized.

Usage with a simulable object

Any FEM_stimulation object can be attached to any NRV_simulable object using the attach_extracellular_stimulation method.

Note

although technically possible, we do not recommand attaching FEM_stimulation to a fascicle. Instead, use a monofascicular nerve object.

The following code snippet shows how to attach a FEM_stimulation to an axon:

my_FEM = nrv.FEM_stimulation()                                          #create an FEM model with default Parameters
my_FEM.reshape_nerve(nerve_d, nerve_l)                                  #set the diameter and length of the nerve
my_FEM.reshape_outerBox(outer_d)                                        #set the diameter of the outer box
my_FEM.reshape_fascicle(fascicle_d1, fascicle_y1, fascicle_z1, ID = 0)  #create a new fascicle with ID 0
my_FEM.reshape_fascicle(fascicle_d2, fascicle_y2, fascicle_z2, ID = 1)  #create a new fascicle with ID 1
my_FEM.add_electrode(my_electrode, my_stimulus)                         #add an electrode
my_axon.attach_extracellular_stimulation(my_FEM)                        #attach the FEM model to the axon
my_result = my_axon(t_sim)                                              #simulate the axon with the FEM model

The following code snippet shows how to attach a FEM_stimulation to a nerve:

my_FEM = nrv.FEM_stimulation()                                          #create an FEM model with default Parameters
my_FEM.add_electrode(my_electrode, my_stimulus)                         #add an electrode
my_nerve.attach_extracellular_stimulation(my_FEM)                       #attach the FEM model to the nerve
my_result = my_nerve(t_sim)                                             #simulate the axon with the FEM model

Note

When attaching a FEM_stimulation to a nerve, the geometrical parameters of the nerve (its diameter, number of fascicles, etc) are overwritten with properties specified of the nerve object. This ensures consistency between the geometrical properties of the FEM model and of the neural model.