this is about importing again:
I received a file reconstructed cell which was used in Neuron simulations (possibly an earlier version). It seems to be in .swc format.
Unfortunately the import through the 3d import tool doesnt work (and cvapp cant read the file either).
I tried to change the first lines of the file, as suggested in the error message, but that didnt help.
Many thanks for any ideas!
Cheers
Ullrich
PS
@Dr Carnevale: You might be familiar with the file as this is the prefrontal cortex cell from the paper Jaffe & Carnevale, J Neurophysiol. 1999 82(6):3268-85, kindly provided by Dr Jaffe.
the prompt:
the start of the file looks like this:ulli@turing:~/neuron/pcmodel/ref_pc/jaffe99> nrngui
NEURON -- Version 5.7 2005-4-21 11:7:7 Main (159)
by John W. Moore, Michael Hines, and Ted Carnevale
Duke and Yale University -- Copyright 2001
oc> 1
1
error ./pfc_full.asc line 17: pid.x[0]=0 (shifted by 4) is not less its index
error ./pfc_full.asc line 18: pid.x[1]=0 (shifted by 7) is not less its index
error ./pfc_full.asc line 19: pid.x[2]=0 (shifted by 10) is not less its index
error ./pfc_full.asc line 20: pid.x[3]=0 (shifted by 13) is not less its index
error ./pfc_full.asc line 21: pid.x[4]=0 (shifted by 11) is not less its index
Notice: ./pfc_full.asc:
The first two points have different types (-1 and 0) but
a single point root section is not allowed.
Changing point id 1 so that it is type -1.
If this is an incorrect repair, then change the file.
/usr/local/nrn/x86_64/bin/nrniv: Arg out of range in user function near line 0
{readfile()}
^
List[11].object(9)
Import3d_SWC_read[0].pt2sec(10.3, NULLobject)
Import3d_SWC_read[0].mksection(1, 2, 3)
Import3d_SWC_read[0].mksections()
and others
Code: Select all
3675
0 -1 -0.89 1.93 0 1.79011 4.26
1 0 -3.27 4.6 1.7 3.96021 7.82
2 1 -5.45 8.5 1.7 4.46793 10.3
3 2 -6.97 11.52 1.7 3.38095 13.5
4 3 -11.09 12.75 1.7 4.29969 11.72
5 0 -5.13 0.49 9.88 2.63013 1.78
6 5 -4.8 -0.03 9.88 0.615873 1.78
7 6 -5.01 -1.8 10.94 2.07379 1.78
8 7 -4.58 -3.58 10.66 1.85248 1.78
9 8 -4.8 -5 13.58 3.25441 1.78
10 9 -4.58 -6.6 15.14 2.24544 1.78
11 10 -4.58 -6.6 14.65 0.490001 1.78
12 11 -3.81 -8.05 16.24 2.2855 1.78
13 12 -3.2 -9.54 16.69 1.67174 1.42
14 13 -3.41 -10.25 16.12 0.934398 1.42
15 14 -2.76 -11.49 17.9 2.26462 1.42
16 15 -2.54 -12.38 18.7 1.21676 1.42
17 16 -1.89 -14.34 19.69 2.29002 1.42
18 17 -1.46 -15.58 19.69 1.31244 1.42
19 18 -0.37 -17.18 19.69 1.936 1.78
20 19 0.93 -17.36 19.69 1.3124 1.42
21 20 2.23 -17.89 19.69 1.40389 1.42
22 21 3.32 -18.07 19.69 1.10476 1.42