Search found 5239 matches

by ted
Fri Jul 20, 2018 7:57 am
Forum: Getting started
Topic: compare vectors pairwise
Replies: 1
Views: 24

Re: compare vectors pairwise

Subtract the lower from the upper.
Integrate over the range of values that are > 0.
The Vector class's methods are your friends.
by ted
Thu Jul 19, 2018 7:58 am
Forum: NEURON Announcements
Topic: High Performance Computing Workshop at SFN 2018 meeting
Replies: 0
Views: 14

High Performance Computing Workshop at SFN 2018 meeting

What: High Performance Computing Resources for Parallel Simulations and Data Analysis: NSG and HPAC When: Saturday, Nov. 3 from 9 AM to noon Where: Downtown San Diego location to be announced SUMMARY This workshop is intended for neuroscientists who need to use high performance computing (HPC) reso...
by ted
Thu Jul 19, 2018 7:49 am
Forum: NEURON Announcements
Topic: NEURON course at the 2018 Society for Neuroscience Meeting
Replies: 0
Views: 13

NEURON course at the 2018 Society for Neuroscience Meeting

What: Using NEURON to Model Cells and Networks When: Friday, Nov. 2 from 9 AM to 5 PM Where: Downtown San Diego location to be announced This course provides a practical introduction to building and using models of neurons and networks with NEURON. Covered topics include basic concepts, workflow fo...
by ted
Thu Jul 19, 2018 7:44 am
Forum: Anatomically detailed models
Topic: Use import3D_swc_read to read the morphology from swc file
Replies: 2
Views: 25

Re: Use import3D_swc_read to read the morphology from swc file

Sections, segments, and how the shapes and sizes of parts of a model are essential concepts. Time to read the documentation:
Conceptual Overview of Sections
https://www.neuron.yale.edu/neuron/stat ... metry.html
by ted
Wed Jul 18, 2018 3:58 pm
Forum: Anatomically detailed models
Topic: Utilizing morphology from IMARIS: help classifying "filaments" as basal/apical dendrites, etc
Replies: 6
Views: 43

Re: Utilizing morphology from IMARIS: help classifying "filaments" as basal/apical dendrites, etc

All those filaments make me think of filariasis--horrible family of parasitic diseases. With regard to your question, often the "root section" of a morphometric reconstruction is just part of the soma, or it may not even be part of the soma at all. The best way to decide what is soma and what is not...
by ted
Wed Jul 18, 2018 1:51 pm
Forum: Anatomically detailed models
Topic: Utilizing morphology from IMARIS: help classifying "filaments" as basal/apical dendrites, etc
Replies: 6
Views: 43

Re: Utilizing morphology from IMARIS: help classifying "filaments" as basal/apical dendrites, etc

I forgot to mention that clicking on the "Select" button (above the radio button for Select One) brings up a list of operations that include All (selects all sections) None (selects no sections) Xor (inverts the current selection) Union (selection becomes the union of two subsets) Intersection (sele...
by ted
Tue Jul 17, 2018 9:38 pm
Forum: Anatomically detailed models
Topic: Utilizing morphology from IMARIS: help classifying "filaments" as basal/apical dendrites, etc
Replies: 6
Views: 43

Re: Utilizing morphology from IMARIS: help classifying "filaments" as basal/apical dendrites, etc

Your choice is to work hard or to work smart. Hard would be to literally rename each section, and that would involve you using a text editor to modify a copy of the original file from Imaris. Very tedious, and P(making multiple, time-wasting mistakes) is 1. Smart would be to import the morphology in...
by ted
Mon Jul 16, 2018 8:10 am
Forum: UNIX/Linux
Topic: compilation with interviews
Replies: 1
Views: 42

Re: compilation with interviews

I can't compile and/or link an interviews program.
Three questions.
1. Was NEURON (including InterViews) ever successfully installed on this computer before?
2. Exactly where did you get the source code?
3. What error messages were generated by configure, make, make install ?
by ted
Thu Jul 12, 2018 5:40 pm
Forum: Getting started
Topic: units check
Replies: 1
Views: 47

Re: units check

In the directory that contains the mod file,
execute the command
modlunit filename
where filename is the name of the mod file. What is modlunit's output?
by ted
Thu Jul 12, 2018 5:39 pm
Forum: Other questions
Topic: Input Sodium Concentration
Replies: 1
Views: 48

Re: Input Sodium Concentration

Sodium concentration where? Intracellular or extracellular? Is there experimental evidence that this happens?
by ted
Sun Jul 08, 2018 1:06 pm
Forum: ModelDB and other online sources of models
Topic: Neuron morphologies with LFPy python module
Replies: 1
Views: 67

Re: Neuron morphologies with LFPy python module

Here are some things to be aware of when reusing one or more model cells implemented by someone else. This list assumes that the code that specifies the properties of the model cell(s) you want to reuse contains no bugs. 1. Is all of the original model specification code (i.e. the statements that sp...
by ted
Thu Jul 05, 2018 1:22 pm
Forum: Other questions
Topic: updating fsin.n for different frequencies
Replies: 5
Views: 52

Re: updating fsin.n for different frequencies

So if you double the frequency, double the number of cycles too. Where's the problem?
by ted
Thu Jul 05, 2018 12:50 pm
Forum: Other questions
Topic: updating fsin.n for different frequencies
Replies: 5
Views: 52

Re: updating fsin.n for different frequencies

I would also like the duration of the stimulation to remain the same for all frequencies and therefore need the number of cycles (fsin.n) to scale with the change in frequency (i.e. fsin.n = fsin.f*duration). fsin.mod isn't going to allow that. It will produce whole cycles, period. I could provide ...
by ted
Thu Jul 05, 2018 12:12 pm
Forum: Other questions
Topic: Using event delivery system with fixed time step method.
Replies: 4
Views: 71

Re: Using event delivery system with fixed time step method.

Would you be kind enough to also explain to me why using h.cvode.solve(h.tstop) leads to h.t=10000000 (despite the fact that h.tstop==5.0) when cvode.active()==0 ? Sounds as reasonable as any other value for t would be. If the adaptive integrator isn't active, why would trying to exercise adaptive ...
by ted
Thu Jul 05, 2018 11:38 am
Forum: Other questions
Topic: updating fsin.n for different frequencies
Replies: 5
Views: 52

Re: updating fsin.n for different frequencies

fsin.mod is not built into NEURON. Nobody knows what is in the particular fsin.mod you are using. Where did you find it?