Main branch starting at line 657 is outside the soma bounding boxes
Making a logical connection to center of nearest soma
I then get a "Possible root branch errors" dialog box that says"
Default logical connection to nearest soma.
Check to physically connect to closest parent in the xy plane.
(Note: may split the parent into two sections)
If I select this option it does create a soma[1](0) and a soma(1) in the .hoc code both of which have many pt3dadd entries with in them:
Code: Select all
proc shape3d_1() {
soma {pt3dclear()
pt3dadd(-1.47, 1.1, 0, 0.18)
pt3dadd(-1.47, 1.65, 0, 0.18)
pt3dadd(-1.65, 2.2, 0, 0.18)
pt3dadd(-2.02, 2.75, 0, 0.18)
pt3dadd(-2.39, 3.49, 0, 0.18)
pt3dadd(-2.75, 4.22, 0, 0.18)
pt3dadd(-3.86, 5.51, 0, 0.18)
pt3dadd(-4.59, 6.61, 0, 0.18)
pt3dadd(-5.51, 7.53, 0, 0.18)
pt3dadd(-6.43, 8.81, 0, 0.18)
pt3dadd(-6.98, 9.73, 0, 0.18)
pt3dadd(-7.71, 10.83, 0, 0.18)
pt3dadd(-8.81, 12.67, 0, 0.18)
pt3dadd(-10.1, 14.5, 0, 0.18)
pt3dadd(-11.01, 16.16, 0, 0.18)
pt3dadd(-11.2, 17.44, 0, 0.18)
pt3dadd(-11.2, 21.3, 0, 0.18)
pt3dadd(-10.65, 23.13, 0, 0.18)
pt3dadd(-10.1, 23.68, 0, 0.18)
pt3dadd(-9.55, 23.87, 0, 0.18)
pt3dadd(-7.89, 24.42, 0, 0.18)
pt3dadd(-6.79, 24.78, 0, 0.18)
pt3dadd(-5.69, 25.15, 0, 0.18)
pt3dadd(-3.49, 25.15, 0, 0.18)
pt3dadd(-2.75, 24.97, 0, 0.18)
pt3dadd(-2.02, 24.42, 0, 0.18)
}
soma[1] {pt3dclear()
pt3dadd(1.85504, 0.69267, 0, 0.925963)
pt3dadd(1.70518, 1.87436, 0, 1.42094)
pt3dadd(1.55533, 3.05605, 0, 1.5322)
pt3dadd(1.40547, 4.23773, 0, 1.3983)
pt3dadd(1.25562, 5.41942, 0, 1.35015)
pt3dadd(1.10576, 6.60111, 0, 1.49653)
pt3dadd(0.955908, 7.7828, 0, 1.50179)
pt3dadd(0.806054, 8.96448, 0, 1.33946)
pt3dadd(0.656199, 10.1462, 0, 1.03173)
pt3dadd(0.506345, 11.3279, 0, 0.832381)
pt3dadd(0.35649, 12.5095, 0, 0.69106)
pt3dadd(0.206636, 13.6912, 0, 0.4867)
pt3dadd(0.0567811, 14.8729, 0, 0.522405)
pt3dadd(-0.0930734, 16.0546, 0, 0.673459)
pt3dadd(-0.242928, 17.2363, 0, 1.13828)
pt3dadd(-0.392782, 18.418, 0, 1.46059)
pt3dadd(-0.542637, 19.5997, 0, 1.68103)
pt3dadd(-0.692491, 20.7814, 0, 1.78193)
pt3dadd(-0.842346, 21.963, 0, 1.5043)
pt3dadd(-0.9922, 23.1447, 0, 1.17581)
pt3dadd(-1.14205, 24.3264, 0, 0.804093)
}
At the bottom of the exported .hoc file it creates a somatic section list.
Code: Select all
somatic = new SectionList()
for i=0, 1 soma[i] somatic.append()
Code: Select all
proc topol() { local i
connect soma[1](0), soma(1)
connect dend(0), soma[1](0.5)
for i = 1, 2 connect dend[i](0), dend(1)
for i = 3, 4 connect dend[i](0), dend[2](1)
connect dend[5](0), soma[1](0.5)
connect dend[6](0), soma(1)
for i = 7, 8 connect dend[i](0), dend[i-1](1)
connect dend[9](0), dend[7](1)
connect dend[10](0), dend[6](1)
for i = 11, 12 connect dend[i](0), dend[10](1)
for i = 13, 14 connect dend[i](0), soma[1](0.5)
for i = 15, 16 connect dend[i](0), dend[i-1](1)
connect dend[17](0), dend[15](1)
connect dend[18](0), dend[14](1)
connect dend[19](0), soma[1](0.5)
for i = 20, 21 connect dend[i](0), dend[19](1)
for i = 22, 23 connect dend[i](0), dend[21](1)
connect apic(0), soma[1](0.5)
for i = 1, 2 connect apic[i](0), apic[i-1](1)
connect apic[3](0), apic[1](1)
connect apic[4](0), apic(1)
for i = 5, 7 connect apic[i](0), apic[i-1](1)
connect apic[8](0), apic[6](1)
for i = 9, 10 connect apic[i](0), apic[8](1)
connect apic[11](0), apic[5](1)
for i = 12, 13 connect apic[i](0), apic[11](1)
connect apic[14](0), apic[4](1)
for i = 15, 16 connect apic[i](0), apic[i-1](1)
connect apic[17](0), apic[14](1)
for i = 18, 19 connect apic[i](0), apic[i-1](1)
connect apic[20](0), apic[18](1)
connect apic[21](0), apic[17](1)
connect apic[22](0), soma[1](0.5)
for i = 23, 24 connect apic[i](0), apic[i-1](1)
connect apic[25](0), apic[23](1)
for i = 26, 27 connect apic[i](0), apic[i-1](1)
connect apic[28](0), apic[26](1)
connect apic[29](0), apic[25](1)
connect apic[30](0), apic[22](1)
basic_shape()
}