Ex_05_axon_with_finite_myelin.m

n_nodes=21;
create('internode',n_nodes+1);              %create a variable named internode with default parameters.
create('node',n_nodes)                      %create a variable named node with default parameters.

%-------------------------------------------------------------------------------------------
global internode node
%-------------------------------------------------------------------------------------------

internode{1}.nseg    =10;                   %       number of segments
internode{1}.L       =1150-1;               %um     Length of internode
internode{1}.dia 	 =10;                   %um     diameter of internode
internode{1}.da_D    =0.6;                  %um     axial diamter of internode for calculating the axonal resistivity
internode{1}.cm		 =0.1/240;              %uf/cm2 internode capacitance
internode{1}.ra	  	 =70;
internode{1}.rm		 =1*240;
internode{1}.vini   =-82;

for i=1:n_nodes
	internode{i+1}.nseg    =10;
	internode{i+1}.L       =1150-1;
	internode{i+1}.dia 	   =10;
	internode{i+1}.da_D    =0.6;
	internode{i+1}.cm	   =0.1/240;
	internode{i+1}.ra      =70;
    internode{i+1}.rm	   =1*240;
    internode{i+1}.vini   =-82;

   
    node{i}.nseg   =1;
    node{i}.L      =1;
    node{i}.dia 	  =3.3;
	node{i}.cm		  =2;
	node{i}.ra	  =70;
    insert(node{i},'Schwarz')
    
    connect(node{i},0,internode{i},1)        %[main, position(0-1), branch, position (0 OR 1)]
    connect(node{i},0,internode{i+1},0)      %[main, position(0-1), branch, position (0 OR 1)]
end
Iinstim(node{1},0,0.0005,100,0) %[variable positon(0-1) amp(uA) pw(us)  delay(us)]
%-------------------------------------------------------------------------------------------
%The parameters that are used in Neurocal are
%.name			%  	    internal use.
%.varnum        %  	    internal use.
%.nseg			% 	    number of segments for the variable.
%.dia       	%(um)	the outer diameter of the variable.
%.da_D  		%		axon/Fiber diameter ratio for calculating the axonal resistance 
                %         - for myelinated axon. if this value is empty(default), 
%                         - .dia will be used instead.
%.dn_D      	%	    node/Fiber diameter ratio for node of Ranvior for calculating the membrane resistance
                %         - and membrane capacitance for myelinated axon. If this value is empty(default), 
                %         - .dia will be used instead.
%.Linter_D      %       Internodal distance / Diameter                
%.L  		    %(um)	the total length of the variable.
%.Lmode         %       1=fix=L, 2 = Linter_D x D x nseg
%.lnodal      	%(um)	Lengh of node of Ranvior for calculating the membrane resistance
                %         - and membrane capacitance for myelinated axon. If this value is empty(default), 
                %         - L/nseg will be used instead.
%.cm	       	%(uf/cm2)for calculating membrane capacitance
%.ra           	%(ohm-cm)for calculating axonal resistance
%.rm           	%(kohm-cm2)for calculating membrane resistance.
%.vini	    	%(mV)
%.model         %
%.vestim		%(mV)   Extracellular voltage (when Ve is not calculated,
%                         - but assigned manually
%.xyz			%(um)   Coordinate of the nodes used for calculating the Ve
%.xyzi    	    % unitless: Vector of the variable (axon) for calculating the coordinate for all nodes
%.xyzc          % um:       The coordinate of the node at the center