Deconstruction of cortical evoked potentials generated by subthalamic DBS (Kumaravelu et al 2018)

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Accession:244262
"... High frequency deep brain stimulation (DBS) of the subthalamic nucleus (STN) suppresses parkinsonian motor symptoms and modulates cortical activity. ... Cortical evoked potentials (cEP) generated by STN DBS reflect the response of cortex to subcortical stimulation, and the goal was to determine the neural origin of cEP using a two-step approach. First, we recorded cEP over ipsilateral primary motor cortex during different frequencies of STN DBS in awake healthy and unilateral 6-OHDA lesioned parkinsonian rats. Second, we used a biophysically-based model of the thalamocortical network to deconstruct the neural origin of the cEP. The in vivo cEP included short (R1), intermediate (R2) and long-latency (R3) responses. Model-based cortical responses to simulated STN DBS matched remarkably well the in vivo responses. R1 was generated by antidromic activation of layer 5 pyramidal neurons, while recurrent activation of layer 5 pyramidal neurons via excitatory axon collaterals reproduced R2. R3 was generated by polysynaptic activation of layer 2/3 pyramidal neurons via the cortico-thalamic-cortical pathway. Antidromic activation of the hyperdirect pathway and subsequent intracortical and cortico-thalamo-cortical synaptic interactions were sufficient to generate cEP by STN DBS, and orthodromic activation through basal ganglia-thalamus-cortex pathways was not required. These results demonstrate the utility of cEP to determine the neural elements activated by STN DBS that might modulate cortical activity and contribute to the suppression of parkinsonian symptoms."
Reference:
1 . Kumaravelu K, Oza CS, Behrend CE, Grill WM (2018) Model-based deconstruction of cortical evoked potentials generated by subthalamic nucleus deep brain stimulation. J Neurophysiol 120:662-680 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex; Thalamus;
Cell Type(s): Neocortex M1 L6 pyramidal corticothalamic GLU cell; Neocortex M1 L5B pyramidal pyramidal tract GLU cell; Neocortex M1 L4 stellate GLU cell; Hodgkin-Huxley neuron; Neocortex layer 4 neuron; Neocortex fast spiking (FS) interneuron; Neocortex primary motor area pyramidal layer 5 corticospinal cell;
Channel(s): I Na,p; I K; I Sodium; I_KD; I Calcium; I T low threshold; I L high threshold; I_AHP;
Gap Junctions: Gap junctions;
Receptor(s): AMPA; Gaba; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Deep brain stimulation; Evoked LFP;
Implementer(s): Kumaravelu, Karthik [kk192 at duke.edu];
Search NeuronDB for information about:  Neocortex M1 L6 pyramidal corticothalamic GLU cell; Neocortex M1 L5B pyramidal pyramidal tract GLU cell; Neocortex M1 L4 stellate GLU cell; AMPA; NMDA; Gaba; I Na,p; I L high threshold; I T low threshold; I K; I Sodium; I Calcium; I_AHP; I_KD; Gaba; Glutamate;
/
cEP_stndbs_4.5hz
cells
dat
data_stndbs_4.5hz
hoc
net
readme.txt
alphasyndiffeq.mod *
alphasynkin.mod *
alphasynkint.mod *
ampa.mod *
ar.mod *
cad.mod *
cal.mod *
cat.mod *
cat_a.mod *
gabaa.mod *
iclamp_const.mod *
k2.mod *
ka.mod *
ka_ib.mod *
kahp.mod *
kahp_deeppyr.mod *
kahp_slower.mod *
kc.mod *
kc_fast.mod *
kdr.mod *
kdr_fs.mod *
km.mod *
naf.mod *
naf_tcr.mod *
naf2.mod *
nap.mod *
napf.mod *
napf_spinstell.mod *
napf_tcr.mod *
par_ggap.mod
pulsesyn.mod *
rampsyn.mod *
rand.mod *
ri.mod *
traub_nmda.mod *
balanal.hoc *
balcomp.hoc *
cell_templates.hoc *
clear.hoc *
finit.hoc *
fortmap.hoc *
gidcell.hoc *
gidcell.ses *
Iintra.dat
init_stndbs_4.5hz.hoc
manage_setup_stndbs_4.5hz.hoc
onecell.hoc *
onecell.ses *
perf.dat
prcellstate.hoc *
printcon.hoc *
run_stndbs_4.5hz.q
spkplt.hoc *
vclampg.hoc *
vcompclamp.hoc *
vcompsim.hoc *
                            
use_load_balance = (load_balance_phase == 3 || load_balance_phase == 5 || load_balance_phase == 7)

{load_file("nrngui.hoc")}
{localloadfile("fortmap.hoc")}
{localloadfile("hoc/parlib.hoc")}
if (fakerank >= 0) pnm.myid += fakerank
if (fakenhost >= 0) pnm.nhost = fakenhost
// til the shift bug in the mod files are fixed (table depends on range variable)
if (1) {
usetable_naf2 = 0
usetable_naf = 0
usetable_naf_tcr = 0
usetable_napf = 0
usetable_napf_spinstell = 0
usetable_napf_tcr = 0
}

calculate_mechanism_complexity(load_balance_phase == 1)
if (load_balance_phase == 1) { pc.runworker() pc.done() quit() }

if (load_balance_phase == 3) {
	read_load_balance_info("splitbal")
}else if (load_balance_phase == 5) {
	read_wholecell_info(wholecell_prefix)
}else if (load_balance_phase == 7) {
	read_multisplit_info(multisplit_prefix)
}

{localloadfile("finit.hoc")}

serial = 0 // override serial set in parlib.hoc
pmesg = 1 && (pc.id == 0)
small_model = 0 // 0 for full model, set to 1 for 40 cells each type
if (use_load_balance) { use_traubexact = 0 } // cannot use with load balance
{localloadfile("hoc/traubcon.hoc")}

{localloadfile("cell_templates.hoc")}
{localloadfile("net/network_specification_interface.hoc")}
if (!serial) {localloadfile("hoc/parlib2.hoc")}
{localloadfile("net/serial_or_par_wrapper.hoc")}
{localloadfile("net/groucho.hoc")}

proc cxrun() {localobj f
	f = new File()
	for pnm.serialize() {
		f.aopen("cxrun.dat")
		f.printf("%d %g\n", pnm.myid, tdat_.x[5])		
		printf("%d %g\n", pnm.myid, tdat_.x[5])		
		f.close
	}
	execerror("stop", "")
}

if (load_balance_phase == 2) {
	print_single_split_load_balance_info("splitbal.dat")
	pc.runworker() pc.done() quit()
}else if (load_balance_phase == 4) {
	print_wholecell_info(wholecell_prefix)
	pc.runworker() pc.done() quit()
}else if (load_balance_phase == 6) {
	print_multisplit_info(multisplit_prefix, multisplit_nhost)
	//execerror("stop", "")
	pc.runworker() pc.done() quit()
}else{
	print_load_balance_info(0)
	if (fakerank >= 0) {cxrun() pc.runworker() pc.done() quit()}
}

want_all_spikes()
mkhist(50)

strdef spkflnm
{sprint(spkflnm,"data_stndbs_4.5hz/spikes/sn%d_%s",pc.id,varfn)}
strdef EFfn
{sprint(EFfn,"data_stndbs_4.5hz/cEP/lfp%d_%s",pc.id,varfn)}
objref mycell, myout


if (pc.id==0) {

{cellobj(0+1+suppyrRS_base).position(-44.512115,-288.4502,-114.95464)}
{cellobj(10+1+suppyrRS_base).position(-145.50232,-220.21071,-14.807648)}
{cellobj(20+1+suppyrRS_base).position(-135.3015,-204.64691,-169.66325)}
{cellobj(30+1+suppyrRS_base).position(192.85052,-380.24155,131.8406)}
{cellobj(40+1+suppyrRS_base).position(108.23099,-193.19618,-28.88527)}
{cellobj(50+1+suppyrRS_base).position(-69.961365,-306.46844,2.1382904)}
{cellobj(60+1+suppyrRS_base).position(-126.76317,-349.0412,73.63861)}
{cellobj(70+1+suppyrRS_base).position(17.876434,-392.57318,-184.23166)}
{cellobj(80+1+suppyrRS_base).position(136.83975,-228.8243,-144.9664)}
{cellobj(90+1+suppyrRS_base).position(217.10684,-253.37321,-104.511475)}
{cellobj(0+1+suppyrFRB_base).position(-156.95486,-400.764,-123.508125)}
{cellobj(5+1+supbask_base).position(74.24451,-303.23157,-116.1904)}
{cellobj(6+1+supaxax_base).position(159.49203,-257.98602,13.694031)}
{cellobj(7+1+supLTS_base).position(214.16748,-158.85056,-46.871277)}
{cellobj(8+1+spinstell_base).position(-22.593521,-563.0592,-41.60768)}
{cellobj(18+1+spinstell_base).position(-6.535553,-555.41614,200.11716)}
{cellobj(4+1+tuftIB_base).position(78.0199,-836.77795,101.45422)}
{cellobj(14+1+tuftIB_base).position(-169.05656,-699.5257,-149.94627)}
{cellobj(24+1+tuftIB_base).position(-196.14322,-618.99036,-32.26822)}
{cellobj(34+1+tuftIB_base).position(80.63248,-638.4526,-74.20749)}
{cellobj(44+1+tuftIB_base).position(-54.30832,-827.1747,197.49628)}
{cellobj(54+1+tuftIB_base).position(137.82693,-639.1483,130.69128)}
{cellobj(64+1+tuftIB_base).position(68.75949,-844.56793,-17.526062)}
{cellobj(74+1+tuftIB_base).position(-49.62796,-765.1999,74.91901)}
{cellobj(4+1+tuftRS_base).position(124.57022,-618.96594,149.29999)}
{cellobj(14+1+tuftRS_base).position(43.805298,-653.1101,33.729034)}
{cellobj(4+1+nontuftRS_base).position(218.09546,-1009.473,32.800903)}
{cellobj(14+1+nontuftRS_base).position(8.876709,-1138.5392,-53.26706)}
{cellobj(24+1+nontuftRS_base).position(83.76218,-1109.6981,-60.14583)}
{cellobj(34+1+nontuftRS_base).position(-198.64621,-1117.9581,71.15402)}
{cellobj(44+1+nontuftRS_base).position(61.173462,-945.93115,-135.42253)}
{cellobj(4+1+deepbask_base).position(-58.878723,-975.1914,75.24432)}
{cellobj(4+1+deepaxax_base).position(-94.66106,-970.7941,-111.01932)}
{cellobj(4+1+deepLTS_base).position(108.40741,-894.9059,109.813965)}

}

if (pc.id==1) {

{cellobj(1+1+suppyrRS_base).position(68.994415,-323.27646,-14.015701)}
{cellobj(11+1+suppyrRS_base).position(18.292847,-289.65424,174.90448)}
{cellobj(21+1+suppyrRS_base).position(-178.39426,-265.50873,94.67468)}
{cellobj(31+1+suppyrRS_base).position(101.04791,-395.51883,51.021423)}
{cellobj(41+1+suppyrRS_base).position(101.486084,-355.88855,10.817566)}
{cellobj(51+1+suppyrRS_base).position(-178.42412,-168.8311,-7.613861)}
{cellobj(61+1+suppyrRS_base).position(91.3757,-372.4083,-85.61394)}
{cellobj(71+1+suppyrRS_base).position(-34.240402,-395.0138,153.42978)}
{cellobj(81+1+suppyrRS_base).position(-148.09134,-328.1176,30.76706)}
{cellobj(91+1+suppyrRS_base).position(-108.53323,-348.2158,-104.65175)}
{cellobj(1+1+suppyrFRB_base).position(-164.24054,-370.5981,-69.36952)}
{cellobj(6+1+supbask_base).position(-158.46652,-382.36386,-42.164856)}
{cellobj(7+1+supaxax_base).position(-50.27484,-301.5633,-211.1414)}
{cellobj(8+1+supLTS_base).position(-21.251953,-345.3103,35.940063)}
{cellobj(9+1+spinstell_base).position(96.36627,-575.9445,48.08081)}
{cellobj(19+1+spinstell_base).position(-29.26123,-449.27667,-132.5968)}
{cellobj(5+1+tuftIB_base).position(189.62802,-735.8586,-73.14259)}
{cellobj(15+1+tuftIB_base).position(117.472565,-841.8336,103.7652)}
{cellobj(25+1+tuftIB_base).position(-190.78674,-658.8572,76.383545)}
{cellobj(35+1+tuftIB_base).position(125.56729,-660.4918,-157.31003)}
{cellobj(45+1+tuftIB_base).position(124.32846,-846.2296,-135.93367)}
{cellobj(55+1+tuftIB_base).position(-224.85104,-709.0252,-74.21399)}
{cellobj(65+1+tuftIB_base).position(-11.948044,-672.041,-154.72537)}
{cellobj(75+1+tuftIB_base).position(-72.33447,-684.8738,-97.51514)}
{cellobj(5+1+tuftRS_base).position(-174.62653,-868.23486,149.90057)}
{cellobj(15+1+tuftRS_base).position(-140.1789,-786.26465,-127.80177)}
{cellobj(5+1+nontuftRS_base).position(-2.3267822,-1029.9238,41.108368)}
{cellobj(15+1+nontuftRS_base).position(-149.65117,-931.544,-166.99469)}
{cellobj(25+1+nontuftRS_base).position(2.737854,-944.37427,129.5622)}
{cellobj(35+1+nontuftRS_base).position(139.0528,-1047.4943,20.605133)}
{cellobj(45+1+nontuftRS_base).position(70.37601,-1093.0101,34.635742)}
{cellobj(5+1+deepbask_base).position(21.539185,-861.45435,128.72955)}
{cellobj(5+1+deepaxax_base).position(-27.389282,-921.52545,-48.059525)}
{cellobj(5+1+deepLTS_base).position(138.80777,-986.3991,96.27374)}

}

if (pc.id==2) {

{cellobj(2+1+suppyrRS_base).position(179.47092,-235.30777,90.582886)}
{cellobj(12+1+suppyrRS_base).position(-77.83786,-264.79883,-163.27718)}
{cellobj(22+1+suppyrRS_base).position(187.12158,-358.96988,71.77655)}
{cellobj(32+1+suppyrRS_base).position(-30.081116,-398.27747,15.802948)}
{cellobj(42+1+suppyrRS_base).position(59.244293,-288.63995,131.60889)}
{cellobj(52+1+suppyrRS_base).position(-117.78175,-261.78137,-31.75563)}
{cellobj(62+1+suppyrRS_base).position(-192.7281,-227.12466,109.69888)}
{cellobj(72+1+suppyrRS_base).position(192.46738,-389.24713,-141.07066)}
{cellobj(82+1+suppyrRS_base).position(-218.68802,-382.01306,50.41516)}
{cellobj(92+1+suppyrRS_base).position(-174.01627,-299.2371,-59.132126)}
{cellobj(2+1+suppyrFRB_base).position(208.9097,-210.0781,-67.696335)}
{cellobj(7+1+supbask_base).position(-87.65546,-152.45306,12.745453)}
{cellobj(8+1+supaxax_base).position(107.75458,-290.8464,-121.35678)}
{cellobj(0+1+spinstell_base).position(169.83966,-529.1555,-42.448105)}
{cellobj(10+1+spinstell_base).position(-85.590515,-515.0604,43.723236)}
{cellobj(20+1+spinstell_base).position(-199.05829,-471.50555,-41.45851)}
{cellobj(6+1+tuftIB_base).position(151.96622,-840.1419,8.837158)}
{cellobj(16+1+tuftIB_base).position(-147.34137,-881.80615,145.34152)}
{cellobj(26+1+tuftIB_base).position(-19.989044,-679.55334,-204.5564)}
{cellobj(36+1+tuftIB_base).position(123.568146,-846.29596,133.84845)}
{cellobj(46+1+tuftIB_base).position(-79.04553,-761.4092,-7.7606964)}
{cellobj(56+1+tuftIB_base).position(145.07343,-646.3427,155.58759)}
{cellobj(66+1+tuftIB_base).position(65.39566,-727.81995,53.72702)}
{cellobj(76+1+tuftIB_base).position(46.77362,-843.9008,146.67194)}
{cellobj(6+1+tuftRS_base).position(-234.89023,-885.0808,16.095093)}
{cellobj(16+1+tuftRS_base).position(-189.71393,-735.0666,-41.17859)}
{cellobj(6+1+nontuftRS_base).position(-132.27051,-980.01587,-59.431396)}
{cellobj(16+1+nontuftRS_base).position(91.600525,-1137.418,82.22662)}
{cellobj(26+1+nontuftRS_base).position(209.65414,-964.85516,-107.495605)}
{cellobj(36+1+nontuftRS_base).position(40.78543,-995.0206,-100.35071)}
{cellobj(46+1+nontuftRS_base).position(-17.825806,-1085.411,-129.22865)}
{cellobj(6+1+deepbask_base).position(-99.12547,-847.9946,143.90317)}
{cellobj(6+1+deepaxax_base).position(42.420197,-966.8096,224.35019)}
{cellobj(6+1+deepLTS_base).position(15.332214,-1148.9395,54.78528)}

}

if (pc.id==3) {

{cellobj(3+1+suppyrRS_base).position(124.32413,-403.38208,-52.37007)}
{cellobj(13+1+suppyrRS_base).position(-18.705688,-351.05334,-96.59285)}
{cellobj(23+1+suppyrRS_base).position(-192.9183,-216.90344,24.806152)}
{cellobj(33+1+suppyrRS_base).position(209.57141,-265.71027,0.9079895)}
{cellobj(43+1+suppyrRS_base).position(-120.7408,-284.13684,-86.69203)}
{cellobj(53+1+suppyrRS_base).position(167.73544,-158.7547,147.04953)}
{cellobj(63+1+suppyrRS_base).position(-153.64328,-399.0986,39.409546)}
{cellobj(73+1+suppyrRS_base).position(-79.84674,-255.59511,104.3486)}
{cellobj(83+1+suppyrRS_base).position(113.11914,-294.9369,-163.06604)}
{cellobj(93+1+suppyrRS_base).position(32.249573,-316.66333,88.36044)}
{cellobj(3+1+suppyrFRB_base).position(-128.30612,-283.4402,-135.36945)}
{cellobj(8+1+supbask_base).position(-154.14392,-153.82675,-112.3139)}
{cellobj(0+1+supLTS_base).position(-192.87914,-205.6247,2.924942)}
{cellobj(1+1+spinstell_base).position(-127.72992,-475.59235,-191.25528)}
{cellobj(11+1+spinstell_base).position(-190.19415,-476.65747,83.45566)}
{cellobj(21+1+spinstell_base).position(145.9353,-510.97534,70.70108)}
{cellobj(7+1+tuftIB_base).position(-89.45372,-876.51843,62.469727)}
{cellobj(17+1+tuftIB_base).position(-161.53589,-670.386,96.44772)}
{cellobj(27+1+tuftIB_base).position(191.3338,-688.72705,130.43369)}
{cellobj(37+1+tuftIB_base).position(136.41486,-854.78754,-121.916794)}
{cellobj(47+1+tuftIB_base).position(-176.14806,-841.45856,-135.97327)}
{cellobj(57+1+tuftIB_base).position(-118.38248,-810.8505,-145.27336)}
{cellobj(67+1+tuftIB_base).position(-187.63799,-768.273,59.58661)}
{cellobj(77+1+tuftIB_base).position(-26.023056,-799.20197,94.34296)}
{cellobj(7+1+tuftRS_base).position(43.439392,-684.13965,111.081604)}
{cellobj(17+1+tuftRS_base).position(52.625214,-798.13525,-51.03064)}
{cellobj(7+1+nontuftRS_base).position(-220.992,-1086.0061,-40.221542)}
{cellobj(17+1+nontuftRS_base).position(-166.61322,-986.8065,122.15875)}
{cellobj(27+1+nontuftRS_base).position(65.029755,-949.11255,145.70233)}
{cellobj(37+1+nontuftRS_base).position(-87.13272,-1052.6566,-124.98233)}
{cellobj(47+1+nontuftRS_base).position(-96.2941,-962.72754,203.77393)}
{cellobj(7+1+deepbask_base).position(5.5352173,-1020.2709,-121.63446)}
{cellobj(7+1+deepaxax_base).position(30.254364,-973.34186,-10.870789)}
{cellobj(7+1+deepLTS_base).position(39.56491,-1122.4824,-196.44968)}
}

if (pc.id==4) {

{cellobj(4+1+suppyrRS_base).position(98.752106,-364.10153,-125.56854)}
{cellobj(14+1+suppyrRS_base).position(-87.05687,-192.50732,61.821014)}
{cellobj(24+1+suppyrRS_base).position(-64.32623,-154.98987,150.29315)}
{cellobj(34+1+suppyrRS_base).position(1.8048248,-231.54239,94.427826)}
{cellobj(44+1+suppyrRS_base).position(15.808411,-216.94821,-15.397583)}
{cellobj(54+1+suppyrRS_base).position(-12.730087,-194.41466,-55.478073)}
{cellobj(64+1+suppyrRS_base).position(-66.63666,-306.2218,-205.39636)}
{cellobj(74+1+suppyrRS_base).position(-72.452896,-194.97388,-164.8378)}
{cellobj(84+1+suppyrRS_base).position(122.75421,-383.5863,75.01886)}
{cellobj(94+1+suppyrRS_base).position(141.99344,-181.5438,-117.95476)}
{cellobj(4+1+suppyrFRB_base).position(-42.396637,-149.96457,-42.46309)}
{cellobj(0+1+supaxax_base).position(178.96814,-289.41034,110.760254)}
{cellobj(1+1+supLTS_base).position(131.63782,-203.08685,176.23138)}
{cellobj(2+1+spinstell_base).position(-159.3211,-464.59073,101.973755)}
{cellobj(12+1+spinstell_base).position(-212.1289,-535.6038,-63.04187)}
{cellobj(22+1+spinstell_base).position(-23.887451,-562.6368,210.99252)}
{cellobj(8+1+tuftIB_base).position(-103.38289,-627.9229,206.94928)}
{cellobj(18+1+tuftIB_base).position(79.63837,-650.8271,-143.29851)}
{cellobj(28+1+tuftIB_base).position(-66.094635,-744.0808,-36.582047)}
{cellobj(38+1+tuftIB_base).position(-160.64282,-703.6181,170.14218)}
{cellobj(48+1+tuftIB_base).position(-170.16263,-757.1808,-133.4379)}
{cellobj(58+1+tuftIB_base).position(86.01489,-655.0299,174.48502)}
{cellobj(68+1+tuftIB_base).position(-155.52988,-704.3753,56.05435)}
{cellobj(78+1+tuftIB_base).position(59.88083,-721.8711,44.103546)}
{cellobj(8+1+tuftRS_base).position(-21.817947,-765.7508,222.31625)}
{cellobj(18+1+tuftRS_base).position(-75.44386,-656.9469,-222.2128)}
{cellobj(8+1+nontuftRS_base).position(-160.62756,-958.0924,-111.133194)}
{cellobj(18+1+nontuftRS_base).position(180.78925,-979.0609,-93.10579)}
{cellobj(28+1+nontuftRS_base).position(43.295105,-991.3267,-111.92349)}
{cellobj(38+1+nontuftRS_base).position(-71.75595,-998.3766,-131.53905)}
{cellobj(48+1+nontuftRS_base).position(108.18817,-1035.8062,72.9884)}
{cellobj(8+1+deepbask_base).position(-23.858337,-623.3599,145.96631)}
{cellobj(8+1+deepaxax_base).position(192.08014,-828.8218,-139.152)}
{cellobj(8+1+deepLTS_base).position(-35.833084,-694.1981,-182.79611)}
}

if (pc.id==5) {

{cellobj(5+1+suppyrRS_base).position(-236.24727,-172.82602,-25.865707)}
{cellobj(15+1+suppyrRS_base).position(73.28134,-293.8255,-163.48868)}
{cellobj(25+1+suppyrRS_base).position(64.7941,-263.2544,93.819214)}
{cellobj(35+1+suppyrRS_base).position(-38.21698,-263.21857,-69.20654)}
{cellobj(45+1+suppyrRS_base).position(38.99829,-369.40497,-21.041122)}
{cellobj(55+1+suppyrRS_base).position(-68.841995,-340.7058,115.77716)}
{cellobj(65+1+suppyrRS_base).position(194.66357,-201.30254,117.394135)}
{cellobj(75+1+suppyrRS_base).position(129.2619,-337.289,-60.785767)}
{cellobj(85+1+suppyrRS_base).position(-138.5597,-374.31003,116.97742)}
{cellobj(95+1+suppyrRS_base).position(-22.920853,-363.87576,182.52454)}
{cellobj(0+1+supbask_base).position(152.08752,-291.98145,160.8977)}
{cellobj(1+1+supaxax_base).position(-187.5162,-407.77753,139.54092)}
{cellobj(2+1+supLTS_base).position(-102.83035,-290.70178,-50.14917)}
{cellobj(3+1+spinstell_base).position(235.24823,-526.622,-4.7712555)}
{cellobj(13+1+spinstell_base).position(-48.148605,-489.66913,37.554535)}
{cellobj(23+1+spinstell_base).position(100.35077,-473.23807,-193.3499)}
{cellobj(9+1+tuftIB_base).position(-192.38147,-703.9649,-88.43263)}
{cellobj(19+1+tuftIB_base).position(65.38684,-884.8892,-200.54817)}
{cellobj(29+1+tuftIB_base).position(154.06467,-787.8104,151.6236)}
{cellobj(39+1+tuftIB_base).position(-140.93365,-805.6212,-108.96811)}
{cellobj(49+1+tuftIB_base).position(42.263214,-790.8118,-81.60901)}
{cellobj(59+1+tuftIB_base).position(49.737152,-675.701,209.69574)}
{cellobj(69+1+tuftIB_base).position(96.40518,-619.34814,-115.40503)}
{cellobj(79+1+tuftIB_base).position(-91.166885,-664.0139,-41.509003)}
{cellobj(9+1+tuftRS_base).position(101.091034,-793.453,-107.528564)}
{cellobj(19+1+tuftRS_base).position(-108.076965,-872.0788,35.979187)}
{cellobj(9+1+nontuftRS_base).position(-89.277176,-948.9118,194.26407)}
{cellobj(19+1+nontuftRS_base).position(-52.27301,-1059.9326,11.370728)}
{cellobj(29+1+nontuftRS_base).position(211.00934,-1034.2402,77.30121)}
{cellobj(39+1+nontuftRS_base).position(104.75632,-1013.7155,158.7291)}
{cellobj(49+1+nontuftRS_base).position(-109.70482,-943.174,-145.20442)}
{cellobj(9+1+deepbask_base).position(-33.469376,-695.4746,209.22116)}
{cellobj(9+1+deepaxax_base).position(-101.236755,-714.9677,40.61609)}
{cellobj(9+1+deepLTS_base).position(194.89938,-891.0918,-53.14096)}
}

if (pc.id==6) {

{cellobj(6+1+suppyrRS_base).position(-52.99437,-398.5226,-55.35251)}
{cellobj(16+1+suppyrRS_base).position(-45.272827,-317.17487,48.98886)}
{cellobj(26+1+suppyrRS_base).position(96.607086,-295.3405,-26.212448)}
{cellobj(36+1+suppyrRS_base).position(215.18774,-230.5534,81.26071)}
{cellobj(46+1+suppyrRS_base).position(154.82846,-410.43585,53.566498)}
{cellobj(56+1+suppyrRS_base).position(79.471954,-202.9715,71.767395)}
{cellobj(66+1+suppyrRS_base).position(-80.20845,-167.40244,10.435455)}
{cellobj(76+1+suppyrRS_base).position(65.267426,-297.422,16.033325)}
{cellobj(86+1+suppyrRS_base).position(-13.948288,-412.11792,-111.832855)}
{cellobj(96+1+suppyrRS_base).position(165.8465,-302.02692,107.811066)}
{cellobj(1+1+supbask_base).position(47.601868,-345.09476,-178.77493)}
{cellobj(2+1+supaxax_base).position(-33.920883,-370.24637,86.003204)}
{cellobj(3+1+supLTS_base).position(-28.608917,-175.11717,144.9473)}
{cellobj(4+1+spinstell_base).position(27.2471,-464.26617,-102.36705)}
{cellobj(14+1+spinstell_base).position(-148.65527,-494.55273,-121.96129)}
{cellobj(0+1+tuftIB_base).position(-36.6604,-830.51117,129.85641)}
{cellobj(10+1+tuftIB_base).position(-146.91455,-718.305,-28.762726)}
{cellobj(20+1+tuftIB_base).position(41.406097,-853.04004,-95.57727)}
{cellobj(30+1+tuftIB_base).position(-40.81604,-676.40857,33.422485)}
{cellobj(40+1+tuftIB_base).position(195.84476,-739.5792,52.64789)}
{cellobj(50+1+tuftIB_base).position(140.78223,-625.59644,14.255463)}
{cellobj(60+1+tuftIB_base).position(-61.9534,-736.9823,-112.03995)}
{cellobj(70+1+tuftIB_base).position(-213.94516,-746.3823,45.427032)}
{cellobj(0+1+tuftRS_base).position(60.62802,-845.1657,-212.0198)}
{cellobj(10+1+tuftRS_base).position(86.08771,-744.1259,-80.44627)}
{cellobj(0+1+nontuftRS_base).position(219.09631,-1040.8064,5.50264)}
{cellobj(10+1+nontuftRS_base).position(-211.16922,-1037.3053,47.343628)}
{cellobj(20+1+nontuftRS_base).position(15.759674,-955.5591,184.6611)}
{cellobj(30+1+nontuftRS_base).position(-163.50827,-1006.9297,-118.95537)}
{cellobj(40+1+nontuftRS_base).position(-152.48703,-935.14417,-146.85544)}
{cellobj(0+1+deepbask_base).position(134.89114,-1129.7101,109.65463)}
{cellobj(0+1+deepaxax_base).position(-102.61711,-989.62085,146.49225)}
{cellobj(0+1+deepLTS_base).position(-181.62862,-725.19366,99.47745)}
}

if (pc.id==7) {

{cellobj(7+1+suppyrRS_base).position(-227.54813,-389.76407,35.841705)}
{cellobj(17+1+suppyrRS_base).position(-215.66379,-346.17078,-48.791077)}
{cellobj(27+1+suppyrRS_base).position(-48.746887,-203.10272,-200.02762)}
{cellobj(37+1+suppyrRS_base).position(-20.012741,-303.6207,210.13269)}
{cellobj(47+1+suppyrRS_base).position(-146.03772,-219.42467,113.37216)}
{cellobj(57+1+suppyrRS_base).position(-21.330948,-396.10345,31.360016)}
{cellobj(67+1+suppyrRS_base).position(-132.14946,-406.86987,1.4658508)}
{cellobj(77+1+suppyrRS_base).position(214.16537,-308.23615,46.559998)}
{cellobj(87+1+suppyrRS_base).position(-147.29628,-258.51453,-45.11299)}
{cellobj(97+1+suppyrRS_base).position(156.49191,-313.1885,147.50076)}
{cellobj(2+1+supbask_base).position(-89.63675,-341.47693,217.05347)}
{cellobj(3+1+supaxax_base).position(68.20105,-258.93094,-55.62967)}
{cellobj(4+1+supLTS_base).position(118.05646,-264.18546,181.125)}
{cellobj(5+1+spinstell_base).position(46.67325,-519.0077,-117.02469)}
{cellobj(15+1+spinstell_base).position(-195.25378,-542.5956,-39.288727)}
{cellobj(1+1+tuftIB_base).position(219.2601,-858.19434,-52.240494)}
{cellobj(11+1+tuftIB_base).position(35.695953,-784.55524,25.55304)}
{cellobj(21+1+tuftIB_base).position(75.15445,-618.1416,-22.292969)}
{cellobj(31+1+tuftIB_base).position(-22.743912,-738.84265,-8.766418)}
{cellobj(41+1+tuftIB_base).position(209.3937,-639.43274,-93.486786)}
{cellobj(51+1+tuftIB_base).position(-109.484726,-676.0025,-9.058975)}
{cellobj(61+1+tuftIB_base).position(-109.13437,-760.6489,60.2146)}
{cellobj(71+1+tuftIB_base).position(-64.631134,-788.185,-178.20758)}
{cellobj(1+1+tuftRS_base).position(141.34012,-639.1433,165.97919)}
{cellobj(11+1+tuftRS_base).position(-110.87442,-827.11743,120.52722)}
{cellobj(1+1+nontuftRS_base).position(134.84555,-971.20386,34.27652)}
{cellobj(11+1+nontuftRS_base).position(160.74902,-1138.1492,-169.16559)}
{cellobj(21+1+nontuftRS_base).position(-77.09485,-1022.1752,11.946777)}
{cellobj(31+1+nontuftRS_base).position(-43.45897,-984.1762,162.8276)}
{cellobj(41+1+nontuftRS_base).position(8.591034,-1027.1497,-158.57628)}
{cellobj(1+1+deepbask_base).position(-38.371063,-1023.3246,-168.47298)}
{cellobj(1+1+deepaxax_base).position(-12.610107,-670.186,178.07077)}
{cellobj(1+1+deepLTS_base).position(92.83136,-933.1782,182.67685)}
}

if (pc.id==8) {

{cellobj(8+1+suppyrRS_base).position(-6.2918396,-371.45084,1.7204895)}
{cellobj(18+1+suppyrRS_base).position(-58.95198,-282.09738,52.08609)}
{cellobj(28+1+suppyrRS_base).position(-20.593643,-410.2902,233.2948)}
{cellobj(38+1+suppyrRS_base).position(233.76474,-325.59888,-35.119415)}
{cellobj(48+1+suppyrRS_base).position(-66.00493,-264.26474,188.33221)}
{cellobj(58+1+suppyrRS_base).position(-137.58817,-157.91101,-160.63086)}
{cellobj(68+1+suppyrRS_base).position(84.18094,-338.64685,-61.158386)}
{cellobj(78+1+suppyrRS_base).position(237.19342,-158.10431,-34.765366)}
{cellobj(88+1+suppyrRS_base).position(52.226593,-293.60968,-232.09322)}
{cellobj(98+1+suppyrRS_base).position(-23.374344,-358.63232,-181.38922)}
{cellobj(3+1+supbask_base).position(-189.1579,-320.62097,-135.13681)}
{cellobj(4+1+supaxax_base).position(96.71661,-227.45592,108.11261)}
{cellobj(5+1+supLTS_base).position(-84.358246,-219.7473,145.2114)}
{cellobj(6+1+spinstell_base).position(74.897675,-530.70874,-86.166626)}
{cellobj(16+1+spinstell_base).position(38.14041,-457.47403,212.74478)}
{cellobj(2+1+tuftIB_base).position(-93.41928,-714.5586,-125.02783)}
{cellobj(12+1+tuftIB_base).position(-200.82271,-640.6656,109.017914)}
{cellobj(22+1+tuftIB_base).position(81.15152,-783.77527,194.80649)}
{cellobj(32+1+tuftIB_base).position(168.16122,-680.93475,99.41202)}
{cellobj(42+1+tuftIB_base).position(-9.755112,-637.8563,33.9227)}
{cellobj(52+1+tuftIB_base).position(229.28683,-785.97003,-15.307159)}
{cellobj(62+1+tuftIB_base).position(-65.94896,-881.9538,-102.2256)}
{cellobj(72+1+tuftIB_base).position(-125.36806,-819.0406,181.97366)}
{cellobj(2+1+tuftRS_base).position(161.41138,-884.677,-160.32712)}
{cellobj(12+1+tuftRS_base).position(-7.0632935,-838.073,-35.075165)}
{cellobj(2+1+nontuftRS_base).position(186.94318,-1131.5116,100.75433)}
{cellobj(12+1+nontuftRS_base).position(135.7898,-1107.9749,-175.47324)}
{cellobj(22+1+nontuftRS_base).position(166.99344,-1089.072,161.3074)}
{cellobj(32+1+nontuftRS_base).position(120.88605,-1067.228,8.405853)}
{cellobj(42+1+nontuftRS_base).position(-58.316803,-936.1247,33.18286)}
{cellobj(2+1+deepbask_base).position(-90.12013,-973.34143,-166.91757)}
{cellobj(2+1+deepaxax_base).position(-172.30447,-820.93677,-74.38582)}
{cellobj(2+1+deepLTS_base).position(-17.829681,-864.9778,-50.255127)}
}


if (pc.id==9) {

{cellobj(9+1+suppyrRS_base).position(-159.25392,-213.4815,156.3353)}
{cellobj(19+1+suppyrRS_base).position(-213.35286,-203.89073,-86.19899)}
{cellobj(29+1+suppyrRS_base).position(-194.89127,-352.53445,87.13684)}
{cellobj(39+1+suppyrRS_base).position(-92.621,-275.01697,45.2948)}
{cellobj(49+1+suppyrRS_base).position(-26.372635,-149.01727,-169.94473)}
{cellobj(59+1+suppyrRS_base).position(160.40598,-232.81796,70.38031)}
{cellobj(69+1+suppyrRS_base).position(42.519043,-176.03412,-19.157562)}
{cellobj(79+1+suppyrRS_base).position(148.78506,-409.26126,127.90997)}
{cellobj(89+1+suppyrRS_base).position(67.1264,-196.00475,-200.42554)}
{cellobj(99+1+suppyrRS_base).position(61.496613,-314.1683,-118.114)}
{cellobj(4+1+supbask_base).position(10.2022705,-396.62012,110.900085)}
{cellobj(5+1+supaxax_base).position(77.77939,-253.36414,-181.87729)}
{cellobj(6+1+supLTS_base).position(-171.59875,-166.63857,86.82529)}
{cellobj(7+1+spinstell_base).position(-188.31816,-560.7106,16.128479)}
{cellobj(17+1+spinstell_base).position(200.75809,-549.9547,19.186127)}
{cellobj(3+1+tuftIB_base).position(135.90906,-703.06354,114.50885)}
{cellobj(13+1+tuftIB_base).position(94.49484,-809.6877,160.43756)}
{cellobj(23+1+tuftIB_base).position(106.94144,-843.64246,-150.78964)}
{cellobj(33+1+tuftIB_base).position(-75.33687,-621.7193,-122.76798)}
{cellobj(43+1+tuftIB_base).position(-46.034363,-740.89215,-11.240448)}
{cellobj(53+1+tuftIB_base).position(-80.13794,-793.63477,131.2351)}
{cellobj(63+1+tuftIB_base).position(-183.42903,-791.0033,-95.1263)}
{cellobj(73+1+tuftIB_base).position(-13.78157,-808.69727,-193.53888)}
{cellobj(3+1+tuftRS_base).position(152.53763,-814.7815,121.312195)}
{cellobj(13+1+tuftRS_base).position(32.099823,-653.6317,-45.214386)}
{cellobj(3+1+nontuftRS_base).position(44.525085,-922.9777,-181.67838)}
{cellobj(13+1+nontuftRS_base).position(-65.15294,-942.43054,154.87137)}
{cellobj(23+1+nontuftRS_base).position(-95.77838,-924.4336,211.35254)}
{cellobj(33+1+nontuftRS_base).position(-172.29071,-1130.7512,-48.507782)}
{cellobj(43+1+nontuftRS_base).position(-99.40213,-1059.1367,-170.25143)}
{cellobj(3+1+deepbask_base).position(117.38614,-830.5193,193.96368)}
{cellobj(3+1+deepaxax_base).position(96.990906,-889.8239,25.414703)}
{cellobj(3+1+deepLTS_base).position(198.8294,-1076.7863,65.44812)}
}








objref fihprog_
// if (pc.id == 0 && pc.nhost < 130) fihprog_ = new FInitializeHandler("progress()")

fihprog_ = new FInitializeHandler("progress()")

proc progress() {

	if (pc.id == 0) {

	print "t=",t
	
	}
	
	myout = new File()
	if (t == 0){
		myout.wopen(spkflnm)
	} else {myout.aopen(spkflnm)}
	for i=0, pnm.idvec.size-1 {
		id = pnm.idvec.x[i]
		//print "id: ", id
		mycell = pc.gid2cell(id)
		//print pnm.spikevec.x[i]
        	myout.printf("%g\t%d\n", pnm.spikevec.x[i], id)
	}
	myout.close
	pnm.spikevec.resize(0)
	pnm.idvec.resize(0)
	
	myout = new File()
	if (t == 0) {
    		myout.wopen(EFfn)
	} else {myout.aopen(EFfn)}
    	for i=0, EFtvec.size-1 {
		myout.printf("%g %g\n", EFtvec.x[i], EF[0].x[i])
    	}
    	myout.close()

	EF[0].resize(0)
	EFtvec.resize(0)
	
	cvode.event(t+1000, "progress()")
	if (t == 0) {layer5_cur_inj()
	calEF1()}
}

proc calEF1(){local depth localobj c
	//print "In cal EF at ", pc.id
	for i=0, 11 { efmm[i] = 0}
	for i=0, cells.count-1 {
		//c = pc.gid2cell(i)
		c = cells.object(i)
		if (strcmp(c.name,"suppyrRS") == 0){
			for j=1, 74 {
				c.comp[j] rdist1=sqrt(((jEFP1x-x3d(1))^2)+((jEFP1y-y3d(1))^2)+((jEFP1z-z3d(1))^2))
				c.comp[j] ar1=area(0.5) 				
				efmm[0] = efmm[0] + (((c.comp[j].i_membrane(0.5))*(ar1*(1e-4)^2))/(4*PI*sigmae*rdist1))
			}
		}
		
		if (strcmp(c.name,"suppyrFRB") == 0){
			for j=1, 74 {
				c.comp[j] rdist1=sqrt(((jEFP1x-x3d(1))^2)+((jEFP1y-y3d(1))^2)+((jEFP1z-z3d(1))^2)) 
				c.comp[j] ar1=area(0.5)
				efmm[1] = efmm[1] + (((c.comp[j].i_membrane(0.5))*(ar1*(1e-4)^2))/(4*PI*sigmae*rdist1))
			}
		}
		
		if (strcmp(c.name,"supbask") == 0){
			for j=1, 59 {
				c.comp[j] rdist1=sqrt(((jEFP1x-x3d(1))^2)+((jEFP1y-y3d(1))^2)+((jEFP1z-z3d(1))^2)) 
				c.comp[j] ar1=area(0.5)
				efmm[2] = efmm[2] + (((c.comp[j].i_membrane(0.5))*(ar1*(1e-4)^2))/(4*PI*sigmae*rdist1))
			}
		}
		
		if (strcmp(c.name,"supaxax") == 0){
			for j=1, 59 {
				c.comp[j] rdist1=sqrt(((jEFP1x-x3d(1))^2)+((jEFP1y-y3d(1))^2)+((jEFP1z-z3d(1))^2)) 
				c.comp[j] ar1=area(0.5)
				efmm[3] = efmm[3] + (((c.comp[j].i_membrane(0.5))*(ar1*(1e-4)^2))/(4*PI*sigmae*rdist1))
			}
		}
		
		if (strcmp(c.name,"supLTS") == 0){
			for j=1, 59 {
				c.comp[j] rdist1=sqrt(((jEFP1x-x3d(1))^2)+((jEFP1y-y3d(1))^2)+((jEFP1z-z3d(1))^2)) 
				c.comp[j] ar1=area(0.5)
				efmm[4] = efmm[4] + (((c.comp[j].i_membrane(0.5))*(ar1*(1e-4)^2))/(4*PI*sigmae*rdist1))
			}
		}
		
		if (strcmp(c.name,"spinstell") == 0){
			for j=1, 59 {
				c.comp[j] rdist1=sqrt(((jEFP1x-x3d(1))^2)+((jEFP1y-y3d(1))^2)+((jEFP1z-z3d(1))^2)) 
				c.comp[j] ar1=area(0.5)
				efmm[5] = efmm[5] + (((c.comp[j].i_membrane(0.5))*(ar1*(1e-4)^2))/(4*PI*sigmae*rdist1))
			}
		}
		
		if (strcmp(c.name,"tuftIB") == 0){
			for j=1, 61 {
				c.comp[j] rdist1=sqrt(((jEFP1x-x3d(1))^2)+((jEFP1y-y3d(1))^2)+((jEFP1z-z3d(1))^2)) 
				c.comp[j] ar1=area(0.5)
				efmm[6] = efmm[6] + (((c.comp[j].i_membrane(0.5))*(ar1*(1e-4)^2))/(4*PI*sigmae*rdist1))
			}
		}
		
		if (strcmp(c.name,"tuftRS") == 0){
			for j=1, 61 {
				c.comp[j] rdist1=sqrt(((jEFP1x-x3d(1))^2)+((jEFP1y-y3d(1))^2)+((jEFP1z-z3d(1))^2)) 
				c.comp[j] ar1=area(0.5)
				efmm[7] = efmm[7] + (((c.comp[j].i_membrane(0.5))*(ar1*(1e-4)^2))/(4*PI*sigmae*rdist1))
			}
		}
		
		if (strcmp(c.name,"nontuftRS") == 0){
			for j=1, 50 {
				c.comp[j] rdist1=sqrt(((jEFP1x-x3d(1))^2)+((jEFP1y-y3d(1))^2)+((jEFP1z-z3d(1))^2)) 
				c.comp[j] ar1=area(0.5)
				efmm[8] = efmm[8] + (((c.comp[j].i_membrane(0.5))*(ar1*(1e-4)^2))/(4*PI*sigmae*rdist1))
			}
		}
		
		if (strcmp(c.name,"deepbask") == 0){
			for j=1, 59 {
				c.comp[j] rdist1=sqrt(((jEFP1x-x3d(1))^2)+((jEFP1y-y3d(1))^2)+((jEFP1z-z3d(1))^2))
                c.comp[j] ar1=area(0.5)				
				efmm[9] = efmm[9] + (((c.comp[j].i_membrane(0.5))*(ar1*(1e-4)^2))/(4*PI*sigmae*rdist1))
			}
		}
		
		if (strcmp(c.name,"deepaxax") == 0){
			for j=1, 59 {
				c.comp[j] rdist1=sqrt(((jEFP1x-x3d(1))^2)+((jEFP1y-y3d(1))^2)+((jEFP1z-z3d(1))^2)) 
				c.comp[j] ar1=area(0.5)
				efmm[10] = efmm[10] + (((c.comp[j].i_membrane(0.5))*(ar1*(1e-4)^2))/(4*PI*sigmae*rdist1))
			}
		}
		
		if (strcmp(c.name,"deepLTS") == 0){
			for j=1, 59 {
				c.comp[j] rdist1=sqrt(((jEFP1x-x3d(1))^2)+((jEFP1y-y3d(1))^2)+((jEFP1z-z3d(1))^2)) 
				c.comp[j] ar1=area(0.5)
				efmm[11] = efmm[11] + (((c.comp[j].i_membrane(0.5))*(ar1*(1e-4)^2))/(4*PI*sigmae*rdist1))
			}
		}
		
		
				
	}
	
	
	efm[0]=efmm[0]+efmm[1]+efmm[2]+efmm[3]+efmm[4]+efmm[5]+efmm[6]+efmm[7]+efmm[8]+efmm[9]+efmm[10]+efmm[11]

	EFtvec.append(t)
	EF[0].append(efm[0])
	cvode.event(t+dt, "calEF1()")

}



    objref stim1[10]
    objref c3
	ktt=0
	for i=0, cells.count-1 {
		//c = pc.gid2cell(i)
		c3 = cells.object(i)
		if (strcmp(c3.name,"tuftIB") == 0){
		c3.comp[61] stim1[ktt]=new IClamp(0.5)
	    c3.comp[61] stim1[ktt].del = 0
		c3.comp[61] stim1[ktt].dur = 1000000	
        ktt=ktt+1		


}

        if (strcmp(c3.name,"tuftRS") == 0){
		c3.comp[61] stim1[ktt]=new IClamp(0.5)
        c3.comp[61] stim1[ktt].del = 0
		c3.comp[61] stim1[ktt].dur = 1000000	
        ktt=ktt+1		


}

}

	proc layer5_cur_inj(){localobj c4
	kt=0
	for i=0, cells.count-1 {
		//c = pc.gid2cell(i)
		c4 = cells.object(i)
		if (strcmp(c4.name,"tuftIB") == 0){
		c4.comp[61] stim1[kt].amp = IN_MATRIX.getval(kt,t/dt)
		
		kt=kt+1
		}

        if (strcmp(c4.name,"tuftRS") == 0){
		c4.comp[61] stim1[kt].amp = IN_MATRIX.getval(kt,t/dt)
		
		kt=kt+1
		}
		}
cvode.event(t+dt, "layer5_cur_inj()")
}





if (nthread > 1 && pc.nhost == 1) { pc.nthread(nthread, 1) }

if (use_traubexact) {
	localloadfile("hoc/traubcon_net.hoc")
	if (pc.id == 0) {
		print "before setting traub exact connection coefficients, setuptime = ", startsw() - setuptime
	}
	define_shape() // force all internal structures to be valid
	reset_connection_coefficients()
}

proc methods() {
	pc.spike_compress(spike_compress, spike_compress != 0, multisend)
	cvode.queue_mode(spike_compress != 0, selfevents)
	cvode.cache_efficient(cacheeffic)
}
methods()

if (load_balance_phase == 7) { pc.multisplit() }

setuptime = startsw() - setuptime
if (pc.id == 0) {print "SetupTime: ", setuptime}