www.neuron.yale.edu

Hi. I'm trying to make it so that I have a variable conductance, increasing along my dendritic branches by a fractional amount, dependent on the distance along the branch it is from the soma. This is my code:

for (x,0) {
xdist1 = distance(x)
if (xdist1 > 500) { xdist1 = 500 }
else {
// gkabar(x) = .0132 + (.000132 * xdist1)
// ghbar(x) = .00003 + (.000009 * xdist1)
}
}

I read the Programmer's Reference and found the following syntax:

For "distance":
Compute the path distance between two points on a neuron. If a continuous path does not exist the return value is 1e20.
distance() with no arguments
specifies the origin as location 0 of the currently accessed section.
distance(x) (0<=x<=1)
returns the distance (in microns) from the origin to this point on the currently accessed section.
To overcome the old initialization restriction, distance(0, x) can be used to set the origin. Note that distance is measured from the centers of segments.

And for "for":
http://www.neuron.yale.edu/neuron/stati ... r.html#for

It gives me an error with regard to "xdist1". Ideas?

Thank you.

Suggest you change your code so that it reports the section name and the distance of every internal node that it finds that satisfies your criterion (you might report
"distance is " whatever
and
"farther than y um"
for your two cases).

Then try it on a toy model with just two or three neurites just to make sure that it works. It's much easier to debug code on a simple model than on a model that has a lot of anatomical complexity.

After you have it reporting distances correctly, revise it to assign the desired conductance density, again using a toy model. Use Model View to verify that it worked.

After you're sure it works on a toy model, then try it on your "real" model. Finally, use Model View to verify that the conductance densities are indeed correct.