www.neuron.yale.edu

Hi there. I am trying to use the ri function, but somehow i am missing the point. here is my file:

load_file ("nrngui.hoc")
create dendrite

create dendrite
dendrite {
L = 4
diam = 2
nseg = 51
cm = 1
Ra = 400
insert pas g_pas=0.0003
e_pas=-80
}


access dendrite

ri(0.01)
ri(1)

============
output:

4.9930963
4.9930963

==> My problem: The values are both the same where i thought they should differ since i am measuring between the same starting at different end points. Hm

Now, I thought ri(x) would give me the resistance "between the center of the segment containing x and its parent segment" (documentation).

Clearly, i have a misconception of what "parent segment" is supposed to mean. I thought it was segment zero, but it seems as if it's just "the next segment over" in other words, ri s the resistance between two ajacent node points, yes?

So my next question would be: How do I make neuron give me the resistance bewteen point a and b, in the same compartment, and between different compartments?

Thank you

tpv wrote:Clearly, i have a misconception of what "parent segment" is supposed to mean. I thought it was segment zero, but it seems as if it's just "the next segment over" in other words, ri s the resistance between two ajacent node points, yes?

Yep.

So my next question would be: How do I make neuron give me the resistance bewteen point a and b, in the same compartment, and between different compartments?

One could get very tricky here with algorithms that traverse the branched tree of a cell
to find a direct path from one point to another, or a bit less tricky by exploiting the
RangeVarPlot class to discover the path for us, but there's nothing wrong with the quick
and dirty approach--

Set all membrane conductances to 0.
Attach an SEClamp with rs = 1e-6 megohm and dur1 = 1e9 ms to point a.

Next you have a choice:

1. Attach an IClamp with del 0, dur 1e9, amp 1 nA to point b.
Run a simulation. The steady state membrane potential at b in mV is the axial resistance
between a and b in megohms.

OR

2. Use the Impedance class or the GUI's Impedance tools to determine Zin (the input
impedance) of the cell at point b for a frequency of 0.1 Hz, or even 1 Hz--either should
be close enough to DC (steady state) for this purpose. The numeric values are in units
of megohms.

Thanks to Alfred P. Doolittle.

--Ted

If Necessity be the Mother of Invention, then surely Gifted Indolence is the absentee Father.

Ok, so for branched structures the "switch of the membrane currents off methods is of course the easiest. Nice.

But for a simple one compartment dendrite, i can't get the resistance with ri? I suppose i can simply do ri(0.01)* dendrite.nseg ?

Hmm.

tpv wrote:But for a simple one compartment dendrite, i can't get the resistance with ri?

No, it is possible to calculate it--"all things are possible with programming," but it's not
always worth the effort if a simpler method is available.

I suppose i can simply do ri(0.01)* dendrite.nseg ?

Not that way, not even if the section is perfectly cylindrical. To see why, try this: Further complications arise if diam is not constant.

If diameter is constant, nseg >= 3, and the locations of the two points are a and b where
1 > b > a > 0, you could do this:
rab = ri(0.5)*int(nseg*(b-a)/L)
ri(0.5) is the axial resistance of a single segment (assuming that nseg >= 3), and
int(nseg*(b-a)/L) is the number of segments between a and b.