Search found 23 matches

by sbrich
Tue May 07, 2019 4:21 pm
Forum: Anatomically detailed models
Topic: Recreating JUST the morphology from an available model (that is coded in an unfamiliar way)
Replies: 3
Views: 411

Re: Recreating JUST the morphology from an available model (that is coded in an unfamiliar way)

Everything worked perfectly... thanks for the help Ted, and my apologies again for overlooking what was a very straightforward solution!
by sbrich
Mon May 06, 2019 10:06 am
Forum: Anatomically detailed models
Topic: Recreating JUST the morphology from an available model (that is coded in an unfamiliar way)
Replies: 3
Views: 411

Re: Recreating JUST the morphology from an available model (that is coded in an unfamiliar way)

Thank you very much Ted! My apologies for the confusion on what ended up being a somewhat trivial question: as I alluded to, the morphology was the one part of this project that I was not directly involved with, as it was done before I joined my lab. Unfortunately the former lab member who was in ch...
by sbrich
Fri May 03, 2019 10:46 am
Forum: Anatomically detailed models
Topic: Recreating JUST the morphology from an available model (that is coded in an unfamiliar way)
Replies: 3
Views: 411

Recreating JUST the morphology from an available model (that is coded in an unfamiliar way)

Hello NEURON forums, My continuing work on a detailed multi-compartment neuron model (that I've already posted quite a few questions on these forums regarding, haha) is nearing it's conclusion! We have a model that we're very happy with up and running, and we're now doing some in silico experiments ...
by sbrich
Tue Mar 12, 2019 1:25 pm
Forum: Anatomically detailed models
Topic: Confusion regarding get_loc and h.cas
Replies: 11
Views: 1207

Re: Confusion regarding get_loc and h.cas

I think we're talking about different things here... let me try and rephrase. I agree with your comment regarding Lists, and am forgetting entirely about everything I wrote pre-Lists. Now everything I'm using is in List form. My synapses are located correctly based on every check I've been able to p...
by sbrich
Tue Mar 12, 2019 1:11 pm
Forum: Anatomically detailed models
Topic: Confusion regarding get_loc and h.cas
Replies: 11
Views: 1207

Re: Confusion regarding get_loc and h.cas

Hi Ted, Happy to report that using Lists and the function you provided solved my problem... for the most part. I'm still curious about one, minor issue (more for my own edification and improving my overall understanding of NEURON than anything else). As it stands, now that everything is a list, when...
by sbrich
Tue Mar 12, 2019 12:41 pm
Forum: Anatomically detailed models
Topic: Confusion regarding get_loc and h.cas
Replies: 11
Views: 1207

Re: Confusion regarding get_loc and h.cas

OK, I think this is starting to make more sense now. I'll go back into my code and redo things with lists as opposed to the N objrefs I was using previously, and then see if I'm able to recover the section info. Here's what I'm still confused about: even if using N objrefs as I was previously doing ...
by sbrich
Tue Mar 12, 2019 10:36 am
Forum: Anatomically detailed models
Topic: Confusion regarding get_loc and h.cas
Replies: 11
Views: 1207

Re: Confusion regarding get_loc and h.cas

Thanks Ted. One last question here. I think I'm doing something similar to what you're suggesting in my code already: namely, since I'm creating a large number of synapses, I use a single object to store them all in. Namely: numsyn=1000 // Number of synapses I'm creating in this run ... objref spike...
by sbrich
Mon Mar 11, 2019 3:30 pm
Forum: Anatomically detailed models
Topic: Confusion regarding get_loc and h.cas
Replies: 11
Views: 1207

Re: Confusion regarding get_loc and h.cas

Thanks Ted... I figured I was confused on something low-level, but didn't realize how confused, haha. To answer your question, I'm only using hoc syntax (I don't know Python... learning it has long been on my ever growing to-do list!). I believe I remember seeing that the h.cas was Python based, but...
by sbrich
Mon Mar 11, 2019 10:35 am
Forum: Anatomically detailed models
Topic: Confusion regarding get_loc and h.cas
Replies: 11
Views: 1207

Re: Confusion regarding get_loc and h.cas

My apologies for the "double post", but was curious to see if anyone could help me with this issue. Thanks!
by sbrich
Thu Mar 07, 2019 3:03 pm
Forum: Anatomically detailed models
Topic: Confusion regarding get_loc and h.cas
Replies: 11
Views: 1207

Confusion regarding get_loc and h.cas

I have an anatomically detailed neuron model and I'm starting to attach some synapses to it in an automated fashion. To check to ensure things are operating as expected, I'm trying to check where each of my various synapses are being placed, for which I'm using the get_loc command (i.e. my synapses ...
by sbrich
Mon Mar 04, 2019 10:13 am
Forum: Other questions
Topic: Minor issue with changing parameter values while NEURON is running
Replies: 6
Views: 452

Re: Minor issue with changing parameter values while NEURON is running

Hi Ted,

I just sent you an e-mail with a "toy" model that should replicate the issue I'm having. Looking forward to seeing what silly oversight of mine is causing this bug, haha.
by sbrich
Fri Mar 01, 2019 11:19 am
Forum: Other questions
Topic: Minor issue with changing parameter values while NEURON is running
Replies: 6
Views: 452

Re: Minor issue with changing parameter values while NEURON is running

nrngui --version
NEURON -- VERSION 7.6.5 master (f3dad62b) 2019-01-11
by sbrich
Fri Mar 01, 2019 10:33 am
Forum: Other questions
Topic: Minor issue with changing parameter values while NEURON is running
Replies: 6
Views: 452

Re: Minor issue with changing parameter values while NEURON is running

Thanks Ted... That's part of why I was so surprised that I was running into this issue! I'll e-mail something over to you now.
Scott
by sbrich
Thu Feb 28, 2019 3:15 pm
Forum: Other questions
Topic: Minor issue with changing parameter values while NEURON is running
Replies: 6
Views: 452

Minor issue with changing parameter values while NEURON is running

Hi all, I've generated a detailed multi-compartment cell model with three parameter sets, each one generated for a different distribution of a particular channel throughout the dendrite. I have my code setup so that, in my init.hoc file, I load the parameters with load_file("L5_Params_~.hoc) and the...
by sbrich
Tue Aug 21, 2018 4:59 pm
Forum: Other questions
Topic: Saving session doesn't save current plot correctly
Replies: 7
Views: 1097

Re: Saving session doesn't save current plot correctly

OK, I'll e-mail you to set something up.