Page 1 of 1

extracellular stimulation

Posted: Sun Jun 30, 2013 10:41 am
by didu_20
i have a question regarding extracellular and stimulation zip file
i created a file of ganglion cell on my own named ganglion.hoc( with a soma and dendrite) and changed to ganglion.hoc in initxstim.hoc and initxrec.hoc.then i complied xtra.mod file and opened initxstim.hoc with neuron but it shows this error -
nrniv: undefined variable e
in /cygdrive/C/nrn73/model/initxstim.hoc near line 1
e// $Id: initxstim.hoc,v 1.2 2005/09/10 23:02:15 ted Exp $
why is that error coming.this is my ganglion cell code.
what should i do ???
please please anyone help me.

Re: extracellular stimulation

Posted: Sun Jun 30, 2013 11:35 am
by shailesh
I guess you forgot to post your ganglion cell code (ganglion.hoc) here.
this is my ganglion cell code.
Do you have some variable/parameter named 'e' in ganglion.hoc?

(p.s. This query seems to have been posted in the wrong section)

Re: extracellular stimulation

Posted: Sun Jun 30, 2013 12:02 pm
by didu_20
this is my code // base definition of ganglion cell


// parameters
DSOMA = 30
LSOMA = 30
LDEND =100

// topology and geometry

create soma, dend // "soma" actually represents soma + axon + some part of dendritic tree
// "dend" represents the remainder of the dendritic tree
access soma
connect dend(0), soma(1)

soma {
nseg = 1
pt3dadd(0,0,0, DSOMA)
pt3dadd(LSOMA,0,0, DSOMA)
insert hh
gnabar_hh= 0.12
gkbar_hh= 0.36


dend {
nseg = 1
pt3dadd(0,0,0, DDEND)
pt3dadd(LDEND,0,0, DDEND)
insert pas
g_pas= 0.002
e_pas= -65
objref gng
gng= new Shape()

Re: extracellular stimulation

Posted: Sun Jun 30, 2013 12:02 pm
by didu_20
please help me in doing this.....the problem is i didnt add any e in my file and rest of the files were kept the from where did this e come????

Re: extracellular stimulation

Posted: Sun Jun 30, 2013 8:32 pm
by ted
The model cell specification you posted above looks OK in that it will create a model cell. The one thing that is missing is a statement that inserts xtra into all sections of the model. So include this statement
forall insert xtra
before the
objref gng
statement, and both initxstim.hoc and initxrec.hoc should work, assuming that you have compiled xtra.mod with mknrndll (nrnivmodl for Linux).

You might as well get rid of the last 4 lines in the file (objref gng etc.) because they are not part of the specification of the biological properties of the model, one of them is superfluous (nrnmainmenu() is already taken care of by the load_file statement at the start of the file), and nrncontrolmenu will only generate an error message.