Search found 51 matches

by roybens
Tue Dec 03, 2013 6:56 pm
Forum: Other questions
Topic: Derivative block calculation per segment or per section
Replies: 3
Views: 1824

Derivative block calculation per segment or per section

Hi When the derivative block is called for a specific mechanism does the state variable have different values for each segment or the same value for the whole section? When i checked this in a toy model i got the same value for all the segments, if this is true i wonder what is the voltage that is u...
by roybens
Sat Nov 23, 2013 1:10 am
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 8414

Re: Getting the full topology (segments level) from hoc

Thanks so much for this solution now the connection works well. Next i set the NODEA and NODEB of the children using GETA and SETA in the branching.mod file as you recommended. I am having difficulties now setting NODEA and NODEB of the Exts' nodes appropriately. If i dont touch them they get a very...
by roybens
Mon Nov 18, 2013 10:26 pm
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 8414

Re: Getting the full topology (segments level) from hoc

I am checking if nchild>1 so if the section does have more than one children there is a scenario where there are two children in the same segment(now that i can use the verbatim i should probably do a better check - that there is no segment that appears more than twice in the v_parent_node array). B...
by roybens
Mon Nov 18, 2013 5:59 pm
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 8414

Re: Getting the full topology (segments level) from hoc

regarding the verbatim used in the ri.mod it helps me a lot since now i can get the fmatrix() in any precision i like and the segments level topology (_nt._v_parent_index) so it has been super helpful and answers the question i asked in the topic. here is the mod file i am using now: NEURON { SUFFIX...
by roybens
Sun Nov 17, 2013 4:49 pm
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 8414

Re: Getting the full topology (segments level) from hoc

So in the loop i didn't change the properties of the last Ext section i am pasting the corrected code: objref somaref,secref,extVec,strFunc,stim,g1 strFunc = new StringFunctions() create Exts[1] proc disperseBranch(){localobj sl,conVec,tempSec,existList strdef fatherStr ext_ind=0 forall{ comps = 0 f...
by roybens
Sun Nov 17, 2013 2:07 pm
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 8414

Re: Getting the full topology (segments level) from hoc

Yes! it does help a lot, my bad
Thanks so much!
by roybens
Fri Nov 15, 2013 12:44 pm
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 8414

Re: Getting the full topology (segments level) from hoc

Thank you very much for this, I tried to implement this but when comparing it to the original code (without splitting the branching) i get different results. So i probably got something wrong: So when i set Ra=0 in the additional nodes then the volt is nan, so i changed it to 0.00000001 but the resu...
by roybens
Sat Nov 09, 2013 2:00 pm
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 8414

Re: Getting the full topology (segments level) from hoc

Hi Ted, Thanks for your time, I probably should have been more clear regarding nt._v_parent_index so its a member of the struct NrnThread defined in nrnoc/multicore.h that holds an array of all the indices of the parents for each segment. My goal is to use GPU and CUDA to simulate neuronal models (h...
by roybens
Fri Nov 08, 2013 1:02 am
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 8414

Getting the full topology (segments level) from hoc

Hi, Is there a way to get the whole topology as in which segment compartments are connected? I saw that "nt._v_parent_index" holds this information but how can i get to it from the hoc file Another question: I am trying to make a modify the dendritic tree so there are no segments that has ...
by roybens
Thu Sep 13, 2012 1:38 am
Forum: Other questions
Topic: Cell where each node has two children or less
Replies: 3
Views: 1577

Re: Cell where each node has two children or less

Hi Ted, Thanks for your reply. I did check they are the same, actually i copied the same code which loaded the same cell, and in one file i applied the function described in the previous post, i can send the hoc files if necessary. Though they dont have the same number of sections since in the origi...
by roybens
Sun Sep 09, 2012 3:24 am
Forum: Other questions
Topic: Cell where each node has two children or less
Replies: 3
Views: 1577

Cell where each node has two children or less

Hello, I am trying to manipulate my cell so each node would not have more than two children. The only section who has more than two children is the soma - (called a_soma in the code). My thought was to make a section array with the size of the number of children that the soma has, connect between th...
by roybens
Thu Jun 07, 2012 5:04 pm
Forum: Other questions
Topic: Right Hand Side (RHS)
Replies: 1
Views: 1103

Right Hand Side (RHS)

Hello,
I am trying to implement a cell with a fork morphology using HH in Matlab.
I am having problems in computing the RHS from fmatrix(). Where can i find the components that make up the RHS (such as cm*dv/dt ion currents and stimulus)?
Best Regards
Roy
by roybens
Thu May 10, 2012 12:58 pm
Forum: Other questions
Topic: Access to the set of linear equations / Hines matrix
Replies: 2
Views: 2347

Re: Access to the set of linear equations / Hines matrix

Thanks a lot it is very helpfull
by roybens
Wed May 09, 2012 1:56 pm
Forum: Other questions
Topic: Access to the set of linear equations / Hines matrix
Replies: 2
Views: 2347

Access to the set of linear equations / Hines matrix

Hello,

Is there any way to access the Hines matrix in hoc?
That is, the almost tridiagonal set of linear equation, used in, e.g. the cnexp model.

Best regards,
Roy
by roybens
Sat Aug 27, 2011 3:53 pm
Forum: NEURON hacks
Topic: Changing NMODL
Replies: 4
Views: 9544

Re: Changing NMODL

Thank you,
I'll take a look into these files.