Search found 27 matches

by Annik
Thu Apr 14, 2016 6:11 pm
Forum: Anatomically detailed models
Topic: swc to hoc conversion
Replies: 4
Views: 6774

Re: swc to hoc conversion

Great, got it to work. Thanks very much!

Annik
by Annik
Tue Apr 12, 2016 8:53 pm
Forum: Anatomically detailed models
Topic: swc to hoc conversion
Replies: 4
Views: 6774

Re: swc to hoc conversion

The second route is more appealing to me. Do you have tips on how to proceed in this direction? I haven't looked at mayavi (using btmorph right now), but I will get some more information about that.
by Annik
Fri Apr 08, 2016 3:09 pm
Forum: Anatomically detailed models
Topic: swc to hoc conversion
Replies: 4
Views: 6774

swc to hoc conversion

This is perhaps an odd question, as it's less about how to make a model work in Neuron and more about how Neuron works. My apologies if this belongs in another section. I have used the geometry of a cell from the modelDB, which was presented as a hoc file. I set up my model to record several variabl...
by Annik
Mon Jan 11, 2016 12:52 am
Forum: Other questions
Topic: Unknown error
Replies: 3
Views: 1255

Re: Unknown error

After renaming the directory to MCM instead, I'm still getting the same message. Any other reasons this might be occurring?
by Annik
Fri Jan 08, 2016 11:09 am
Forum: Other questions
Topic: Unknown error
Replies: 3
Views: 1255

Unknown error

Hi, I'm getting an error message I don't understand. /home/t/tyrell/annik/Multi Compartment Model/x86_64/special: line 13: 5798 Killed "${NRNIV}" -dll "/home/t/tyrell/annik/Multi Compartment Model/x86_64/.libs/libnrnmech.so" "$@" What is the problem/how should I troubleshoot this? Thanks, Annik
by Annik
Thu Nov 19, 2015 1:50 pm
Forum: Anatomically detailed models
Topic: Issues with ion valence?
Replies: 3
Views: 6436

Re: Issues with ion valence?

Thanks for your quick reply. I have removed the ion management statements and the problem persists. In mod files using Cl I have appropriate statements i.e. USEION cl READ icl, ecl, clo WRITE cli VALENCE -1 (and as you mentioned this mod file contains a kinetic block to solve for cli in terms of ion...
by Annik
Wed Nov 18, 2015 4:14 pm
Forum: Anatomically detailed models
Topic: Issues with ion valence?
Replies: 3
Views: 6436

Issues with ion valence?

Hi, I have built a multicompartment model to observe how Cl is regulated following GABAergic input. I have written the code such that the user may specify where GABAergic synapses are inserted into the cell (at the soma, in proximal dendrites or distal dendrites) using a prompt window which then cal...
by Annik
Tue Sep 30, 2014 5:07 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: xvalue for strings?
Replies: 4
Views: 1676

Re: xvalue for strings?

Got it. The code below works:

Code: Select all

	proc read_TC() {
		TC_file_loc.chooser("", "Choose a File to Read", "*.txt", "Execute")
		if (TC_file_loc.chooser()) {
			strdef str
			str = TC_file_loc.getname()
			TC_read.ropen(str)
		}
	}	
by Annik
Tue Sep 30, 2014 4:29 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: xvalue for strings?
Replies: 4
Views: 1676

Re: xvalue for strings?

Great, I got a button to bring up a window to choose a file using the following code (as per the programmer's reference): objref TC_f TC_f = new File() proc read_TC() { TC_f.chooser("r", "Select a File to Read", "*.txt", "Execute") if (TC_f.chooser()) { str = TC_f.getname(str) xopen(str) } } With xb...
by Annik
Thu Sep 25, 2014 4:11 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: xvalue for strings?
Replies: 4
Views: 1676

xvalue for strings?

Hi, I was wondering if it is possible to create a field editor like xvalue, but which takes a string input like a file name. I'm trying to create a prompt window which asks the user to specify a binary file to be read in before running the simulation. Is such a thing possible?

Thanks,
Annik
by Annik
Tue May 13, 2014 3:43 pm
Forum: The GUI
Topic: Controlling the size of a panel
Replies: 2
Views: 5697

Re: Controlling the size of a panel

Found it -- used VBox().
by Annik
Tue May 13, 2014 3:10 pm
Forum: The GUI
Topic: Controlling the size of a panel
Replies: 2
Views: 5697

Controlling the size of a panel

I was wondering if there is a way to specify the size of a panel created with xpanel? That is, setting the size as one would with saving a window

Code: Select all

save_window = new Graph(0)
save_window.size(0,tstop,-90, -50)
{save_window.view(0, -90, tstop, 40, 1020, 30, 300.48, 200.32)}    
Thanks
by Annik
Thu May 08, 2014 12:02 pm
Forum: NEURON + Python
Topic: Having python read from a NEURON binary file
Replies: 7
Views: 4698

Re: Having python read from a NEURON binary file

I'm somewhat new to this, so I was only using a binary file because I was using vwrite. I'm certainly not set on it. How can I get neuron to record data in another file type?
by Annik
Thu May 08, 2014 11:03 am
Forum: NEURON + Python
Topic: Having python read from a NEURON binary file
Replies: 7
Views: 4698

Re: Having python read from a NEURON binary file

It is indeed a binary file. If I run the python code with def read_list_header(self): sec_list_name = self.file.read(4) self.file.seek(4,1) num_sections = struct.unpack('d', self.file.read(8))[0] self.file.seek(8,1) return (sec_list_name, num_sections) (sec_name, num_sections) = self.read_list_subhe...
by Annik
Tue May 06, 2014 11:58 am
Forum: NEURON + Python
Topic: Having python read from a NEURON binary file
Replies: 7
Views: 4698

Re: Having python read from a NEURON binary file

Sorry, I should have given more information. The hoc code continues as follows: //output somatic section subheader runfile.printf("%s", "soma") runfile.printf("%d", 1) for i = 0,soma_listv.count()-1 { for j = 0,soma_listv.o(i).count()-1 { soma_listv.o(i).o(j).vwrite(runfile) soma_listicl.o(i).o(j).v...