NEURON changes dendrite diameter to default value
Posted: Tue Mar 02, 2021 11:54 am
Hi all,
a student of mine is introducing herself to NEURON (I am usally not using the software myself) and she observed something strange and I was also able to reproduce the issue.
She took a .swc file from neuromorpho and used the CellBuilder tool to create an anatomically detailed neuron model. She stored the result in a .hoc file.
Scenario 1:
I use the GUI and use File -> load hoc -> select file 'geom_test.hoc'
I type 'forall psection()' to the neuron command window to see the sizes of each section.
Result: The dendrites alle have different diameters in the range of 1 to 10 um. -> that looks good
Scenario 2:
I type 'load_file("geom_test.hoc") into the command field.
I type 'forall psection()' to the neuron command window to see the sizes of each section.
Result: All dendrites have a diameter of 500um.
My question is: Why do Scenario 1 and 2 not produce the same result? What is lost when using the load_file command?
Thanks for your help!
Laura
PS.: I would post the geom_test.hoc file but it is very long.
a student of mine is introducing herself to NEURON (I am usally not using the software myself) and she observed something strange and I was also able to reproduce the issue.
She took a .swc file from neuromorpho and used the CellBuilder tool to create an anatomically detailed neuron model. She stored the result in a .hoc file.
Scenario 1:
I use the GUI and use File -> load hoc -> select file 'geom_test.hoc'
I type 'forall psection()' to the neuron command window to see the sizes of each section.
Result: The dendrites alle have different diameters in the range of 1 to 10 um. -> that looks good
Scenario 2:
I type 'load_file("geom_test.hoc") into the command field.
I type 'forall psection()' to the neuron command window to see the sizes of each section.
Result: All dendrites have a diameter of 500um.
My question is: Why do Scenario 1 and 2 not produce the same result? What is lost when using the load_file command?
Thanks for your help!
Laura
PS.: I would post the geom_test.hoc file but it is very long.