I am trying to import a morphology (from an .swc file) through cell builder. NEURON says that there are file translation problems. The terminal emits an error message saying that there is more than one tree. Any information on this appreciated.
Thanks in advance
Morphology import error
-
- Site Admin
- Posts: 6300
- Joined: Wed May 18, 2005 4:50 pm
- Location: Yale University School of Medicine
- Contact:
Re: Morphology import error
If two or more intact cell morphologies are present, Import3d will just launch multiple CellBuilders (one for each cell morphology), and will not generate an error message. You got an error message, so most likely you have a morphology file in which at least one neurite is not connected to its parent. Tell the person who gave you the data.
Re: Morphology import error
Thanks so much for taking the time to explain me the problem. The morphology as viewed using Neurolucida/HBP Neuron Morphology viewer looks good without any issues. I don't see any point which is not connected to the parent. Only when I import it in NEURON, there are a few points without any parent. Is there any way to solve this issue?
Thanks in advance,
Shyam
Thanks in advance,
Shyam
-
- Site Admin
- Posts: 6300
- Joined: Wed May 18, 2005 4:50 pm
- Location: Yale University School of Medicine
- Contact:
Re: Morphology import error
Can you send me ted dot carnevale at yale dot edu the morphology file?
-
- Site Admin
- Posts: 6300
- Joined: Wed May 18, 2005 4:50 pm
- Location: Yale University School of Medicine
- Contact:
Re: Morphology import error
It's a bad file. Look at the error messages that NEURON prints to the interpreter window.
Open the file with a text editor and you'll see that the messages are correct (the last item in each referenced line ends with -1, which is SWC's way of saying that the line is the first coordinate of a branch that is the root of a tree.
The problem lies either with the software that was used to generate or capture the swc data, or with the person who used the hardware and software that was employed to generate or capture the swc data (who would have failed to use it properly). I can't help you with this.
Code: Select all
oc>warning ./morphology.swc: more than one tree:
root at line 35
root at line 36
root at line 76
root at line 120
root at line 164
root at line 208
root at line 258
etc.
for more than 20 lines.
The problem lies either with the software that was used to generate or capture the swc data, or with the person who used the hardware and software that was employed to generate or capture the swc data (who would have failed to use it properly). I can't help you with this.