Search found 34 matches

by reza_rzm
Fri Jan 15, 2010 3:02 pm
Forum: Getting started
Topic: load several geomtery file
Replies: 14
Views: 16401

Re: load several geomtery file

Dear Ted,
thanks so much for your prompt reply, and thanks for this link :viewtopic.php?f=28&t=1391:
by reza_rzm
Fri Jan 15, 2010 9:49 am
Forum: Getting started
Topic: load several geomtery file
Replies: 14
Views: 16401

Re: load several geomtery file

Hello,

I have tried to write a shell script to run Neuron and unfortunately, never succeed. I was wondering if you already have a solution for that, you can share with me!

i am using Neuron 7.1, winxp (32 -bit) and don't have cygwin!

Thanks in advance
by reza_rzm
Tue Jan 22, 2008 1:57 pm
Forum: Getting started
Topic: d_lambda rule and one error
Replies: 3
Views: 2153

Thanks Ted, I used the same code as "" http://www.neuron.yale.edu/neuron/static/docs/d_lambda/d_lambda.html During reconstruction the cell by Neurolucida, i had different values for the diameters of the dendritic section. But i don't see any message for dendritic section "diam is not constant". for ...
by reza_rzm
Mon Jan 21, 2008 1:06 pm
Forum: Getting started
Topic: d_lambda rule and one error
Replies: 3
Views: 2153

d_lambda rule and one error

Hello, I'm developing a multicompartment model, from a reconstructed cell. my code has the following structure : load_file("nrngui.hoc") load_file("mycell.hoc") // this is my cell // define biophysics xopen("fixnseg.hoc") geom_nseg() From Tools/Distributed Mechanism/Viewers /Shape name soma has sele...
by reza_rzm
Sat Feb 17, 2007 2:00 pm
Forum: Getting started
Topic: error in "import 3D data"
Replies: 7
Views: 5756

some points from Hines: Question about multiple contours for soma: Answer: The contours represent slices through the soma. After viewing them in the Import3D, decide which one to retain and get rid of the rest. Or else get rid of all of them and define a new contour from a different projection that ...
by reza_rzm
Fri Feb 16, 2007 5:38 pm
Forum: Getting started
Topic: error in "import 3D data"
Replies: 7
Views: 5756

Dear Ted, Thank you very much. 1- in the previous post i put the data of one branch of the cell. and exactly i see the same error! I hope somebody can find out the problem. 2- Multiple contours for soma: export data creates multiple CellBuilder , then the problem is which of them ? 2- and if we take...
by reza_rzm
Fri Feb 16, 2007 4:23 pm
Forum: Getting started
Topic: error in "import 3D data"
Replies: 7
Views: 5756

please try, 3D tools with the following file. do you know, where is error come from? name : dend1.ASC ; V3 text file written for MicroBrightField products. (ImageCoords) ("CellBody" (Color Green) (CellBody) (-1362.88 -69.95 -5.02 0.12) ; (-1361.19 -63.14 -5.02 0.12) ; 2, 2 (-1359.51 -59.88 -5.02 0.1...
by reza_rzm
Fri Feb 16, 2007 12:36 pm
Forum: Getting started
Topic: error in "import 3D data"
Replies: 7
Views: 5756

One more:

for "soma", should we use one conture or more, to specify the shape of soma?


Any comment?

please!

await for your reply
by reza_rzm
Fri Feb 16, 2007 8:43 am
Forum: Getting started
Topic: error in "import 3D data"
Replies: 7
Views: 5756

error in "import 3D data"

Hi, I have morphological data of a cell, which is obtained by Neurolucida. to import these data, i'm using Tool/Miscellaneous/import 3D (I have *.ASC data file) but, i get following error oc> Device or resource busy nrniv: errno set during call of File[0].choser near line 2 {readfile()} ^ 6000 lines...
by reza_rzm
Sat Nov 11, 2006 12:36 pm
Forum: Getting started
Topic: after importing morphological data
Replies: 9
Views: 7225

Dear Ted, Thanks again. Unfortunately, i don't get the point. for nseg=1,3,9,15,19, and i obtain different area for soma, but after nseg=19 - nseg=23,33,... - area for soma are equal. so, please tell me, which number should i take as a section area? should we change nseg until we reach to a converge...
by reza_rzm
Fri Nov 10, 2006 4:45 pm
Forum: Getting started
Topic: after importing morphological data
Replies: 9
Views: 7225

Thanks ted, Ok.different method to calculate area when we are using stylized or 3-d specification. I use morphological data, so i use 3-d specification method for my cell after importing data, oc> soma print nseg, soma(0.5)*nseg result is oc> 1 3171.43 if i change nseg for soma, i obtain oc> soma pr...
by reza_rzm
Thu Nov 09, 2006 4:47 pm
Forum: Getting started
Topic: after importing morphological data
Replies: 9
Views: 7225

Thanks for all your points. Let me ask other question. 1- I have imported my morphological data to Neuron. 2- I have inserted passive and active property in the cell 3- then,for d_lambda rule, i use the following code "http://hines.med.yale.edu/neuron/static/docs/d_lambda/d_lambda.html" in a file ca...
by reza_rzm
Mon Nov 06, 2006 9:19 pm
Forum: Getting started
Topic: trac a branch!
Replies: 3
Views: 3604

Thanks ted,

Yes, probably thats the way to use SectionRef. But i can not find a good way.

Can you give me some advices?

Thanks,
by reza_rzm
Mon Nov 06, 2006 3:46 pm
Forum: Getting started
Topic: trac a branch!
Replies: 3
Views: 3604

trac a branch!

Hi, Look at the following scehamtic bracnh of cell! dend1[3] / dend1[5] dend1[2]------ / / \ -- dend1[4]--- dend1[1]---- \ dend1[6] / \dedn1[7] / dend1[0]-- \ dend1[9]--dend1[10] \ / dend1[8]---- dend1[12] \ / dend1[11]-- \dedn1[13]-dend1[14] for this branch,i like to create a section list, which co...
by reza_rzm
Sat Oct 21, 2006 4:40 pm
Forum: Getting started
Topic: after importing morphological data
Replies: 9
Views: 7225

Thanks Ted, 1-Could you tell me is it a good idea, to divide a section with length,e.g, more than 100 um to 2 or 3, to have section with length <= 100 um ? 2- And, connect a axon, e.g with 10 section, to soma, for obtaining more accurate result, of firing spike? And a different question, would you p...