Exporting a hoc file from import3d

Managing anatomically complex model cells with the CellBuilder. Importing morphometric data with NEURON's Import3D tool or Robert Cannon's CVAPP. Where to find detailed morphometric data.
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sandeepb
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Joined: Tue Apr 21, 2015 2:16 am

Exporting a hoc file from import3d

Post by sandeepb » Fri Jan 01, 2016 11:35 am

Hi,

I am trying to export a hoc file from import 3d tool using the cellbuilder, the cell builder dialog is not showing up and i came across the following errror

id2line (func) returns no value
near line 1
{cbexport()}
^
Import3d_SWC_read[0].id2line(2)
Import3d_GUI[0].chk_valid()
Import3d_GUI[0].cbexport()

Can someone help me in solving this

Thank you

ted
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Location: Yale University School of Medicine
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Re: Exporting a hoc file from import3d

Post by ted » Fri Jan 01, 2016 3:11 pm

Sounds like a bug. What version of NEURON are you using--see the first line that NEURON prints to its terminal after nrngui starts--and under what OS (MSWin, Linux, OS X)?

sandeepb
Posts: 6
Joined: Tue Apr 21, 2015 2:16 am

Re: Exporting a hoc file from import3d

Post by sandeepb » Fri Jan 01, 2016 10:10 pm

Hi,
I am using Neuron 7.4 Version, with Linux 14.04 as a Platform, Please see below response for "nrngui" command.

nrngui
NEURON -- Release 7.4 (1351:8f462ea7e030) 2015-07-21
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits

nrniv: unable to open font "*helvetica-medium-r-normal*--14*", using "fixed"

ted
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Re: Exporting a hoc file from import3d

Post by ted » Sat Jan 02, 2016 3:43 pm

That's a reasonably recent implementation of NEURON. I haven't heard any recent reports of the problem you encountered, so please let me know:
1. Was Import3d_GUI able to read your morphology file without generating an error message?
2. Was it able to export to a CellBuilder without generating an error message?

Finally, I'll have to try to reproduce the symptom you ran into, so could you please email me
ted dot carnevale at yale dot edu
the original morphology file that you were working with?

sandeepb
Posts: 6
Joined: Tue Apr 21, 2015 2:16 am

Re: Exporting a hoc file from import3d

Post by sandeepb » Sun Jan 03, 2016 5:45 am

Yes, I can successfully import morphology file without an error.
Not able to export to cell builder

ted
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Re: Exporting a hoc file from import3d

Post by ted » Sun Jan 03, 2016 3:53 pm

With NEURON 7.4 (1327:d5bf062d0b56) 2015-04-25 under CentOS 6.7, Import3d generated these two comments when it read the swc file

One point section Import3d_Section[2] ending at line 9 has been removed
One point section Import3d_Section[1] ending at line 8 has been removed

but there was no problem at all with exporting to a CellBuilder.

I didn't see any comments in the mercurial repository about changes to Import3d or the CellBuilder since April 2015, but I updated anyway to the most recent development version of NEURON 7.4 (1377:883b55ed82fb) 2015-12-28. With this new version, I got the same results as before--the comments were identical, and the two hoc files exported from the CellBuilder were also
identical to those that were generated with (1327:d5bf062d0b56) 2015-04-25.

So maybe there is a problem that is isolated to the version you are running. If you're going to use Import3d a lot, it might be a good idea to install from the most recent development code.

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