Search found 13 matches

by ssothro
Fri May 26, 2006 10:42 pm
Forum: Getting started
Topic: DC Space contanst
Replies: 3
Views: 5261

Hi Ted, I have a question on the previous post regarding the DC space constant (lambda= sqrt ( (d*Rm)/4*Ri)) ). In an existing cell model, is there a way to calculate Rm? Can one utilize the extracellular mechansim, use i_membrane for transmembrane current and divide the resting mebrane potential by...
by ssothro
Thu May 11, 2006 6:27 pm
Forum: Getting started
Topic: Boundary conditions
Replies: 3
Views: 4037

"Nodes at 0 and 1 have no associated membrane or cytoplasm, and v at those locations is calculated as the weighted average of v at adjacent internal nodes." What if a section does not have two adjacent nodes, e.g. last node of a cable. In that case what happens to the end? Its potential becomes just...
by ssothro
Thu May 11, 2006 4:12 pm
Forum: Getting started
Topic: Boundary conditions
Replies: 3
Views: 4037

Boundary conditions

Hi all,
I would like to ask what type of boundary conditions NEURON applies. If for example, a single section is created, how are its 0 and 1 ends terminated?

Thank you in advance.
by ssothro
Wed May 10, 2006 4:00 pm
Forum: Getting started
Topic: Measuring longitudinal intracellular current
Replies: 3
Views: 4023

"Code:
dend { iax = ( v(0.01) - v(0) ) / ri(0.01) }

This assumes that dend.nseg < 100. "

What if section dend has nseg=1? Is the above formula still valid?
by ssothro
Mon May 08, 2006 6:05 pm
Forum: Getting started
Topic: Measuring longitudinal intracellular current
Replies: 3
Views: 4023

Measuring longitudinal intracellular current

Hi all,
I am interested in the longitudinal current that flows intracellularly through the Ra resistors in a cell model. Does NEURON keep this current in a variable accessible to the user? If not is there an easy way to calculate this current?

Thanks.
by ssothro
Thu Apr 27, 2006 2:18 pm
Forum: Getting started
Topic: Cathodic and anodic extracellular stimulation
Replies: 1
Views: 3907

Cathodic and anodic extracellular stimulation

Hi, I am trying to simulate extracellular stimulation of a neuron using the extracellular mechanism and e_extracellular. I guess, in order to simulate cathodic stimulation, e_extracellular should have negative values and for anodic stimulation, e_extracellular should be positive. Is that correct? Be...
by ssothro
Tue Apr 18, 2006 6:12 pm
Forum: Other questions
Topic: Extracellular stimulation
Replies: 1
Views: 2772

Extracellular stimulation

Hi all, I am trying to apply the extracellular mechanism to a reconstructed pyramidal cell available in MODELDB. I want to simulate voltage-controlled extracellular stimulation, so I am giving to e_extracellular potentials values that correspond to field potentials I have calculated using a Finite E...
by ssothro
Tue Apr 11, 2006 3:17 pm
Forum: Other questions
Topic: Firing threshold calculation
Replies: 1
Views: 4109

Firing threshold calculation

Hi all, I was wondering whether there is a predefined procedure or mechanism in NEURON that calculates the firing threshold for a cell model, when intracellular stimulation of given pulse width is used. I guess one can implement a .hoc file that will run a bunch of simulations and will monitor excit...
by ssothro
Tue Apr 04, 2006 7:05 pm
Forum: Anatomically detailed models
Topic: 3D points of a segment
Replies: 1
Views: 3846

3D points of a segment

Hi all, I am trying to understand how 3D morphological points for a given segment can be correlated with compartments of the segment. For example, if we have the following scenario create a access a pt3dclear() pt3dadd(x1, y1, z1, diam1) ... pt3dadd(x10,y10, z10, diam10) In that case segment "a" has...
by ssothro
Tue Apr 04, 2006 12:12 am
Forum: Getting started
Topic: How to move neuron in space without changing its dimensions
Replies: 5
Views: 6401

Apart from moving a reconstructed cell is there an easy way to rotate it in 3D space?

Thanks
by ssothro
Wed Mar 22, 2006 2:28 pm
Forum: Other questions
Topic: Question on Linear Mechanism
Replies: 2
Views: 3493

So, the value of the transverse conductors will vary depending on the area of the respective segments. In my model of myelinated fiber, nodes for example have smaller areas than internodes, so the transverse conductors that correspond to nodes will have a smaller value than the ones that correspond ...
by ssothro
Sat Mar 18, 2006 6:17 pm
Forum: Other questions
Topic: Question on Linear Mechanism
Replies: 2
Views: 3493

Question on Linear Mechanism

Hi all, I am trying to use the linear mechanism in order to model ephaptic interactions. According to the online reference, arguments of the linear mechanism are in units/cm2. For example, the conductance vector g has dimensions of S/cm2. In my case, this vector represents the transverse conductance...
by ssothro
Tue Feb 28, 2006 6:08 pm
Forum: Getting started
Topic: Passing strings as parameters in proc()
Replies: 1
Views: 3196

Passing strings as parameters in proc()

Hi, I am trying to define a procedure in a hoc file that will take as a parameter section names. E.g. If I have a soma and an axon section I would like to have something like that: foo() { $1.L=10 ... } foo(soma) Is there a way to do that? I tried to do the above implementation, but the compiler ret...