Computational Surgery (Lytton et al. 2011)

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Accession:140881
Figure 2 in Neocortical simulation for epilepsy surgery guidance: Localization and intervention, by William W. Lytton, Samuel A. Neymotin, Jason C. Wester, and Diego Contreras in Computational Surgery and Dual Training, Springer, 2011
Reference:
1 . Lytton WW, Neymotin SA, Wester JC, Contreras D (2011) Neocortical simulation for epilepsy surgery guidance: Localization and intervention Computational Surgery and Dual Training
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Epilepsy;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu];
/
b11aug17
data
readme.txt
intf6_.mod *
misc.mod *
nstim.mod *
stats.mod *
vecst.mod *
col.hoc
declist.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
gload.hoc
grvec.hoc
init.hoc
labels.hoc
local.hoc *
misc.h *
mosinit.hoc
network.hoc
nqs.hoc
nqs_utils.hoc *
nqsnet.hoc *
nrnoc.hoc *
params.hoc
run.hoc
setup.hoc *
simctrl.hoc *
spkts.hoc *
stats.hoc
stdgui.hoc *
syncode.hoc
                            
// $Id: gload.hoc,v 1.16 2011/08/17 15:25:16 billl Exp $

//* setup number of cells setcpercol - set # of cells per column
double cpercol[CTYPi]
scale = 4
E5RNumF=E5BNumF=1
proc setcpercol () { local i,jj // (/u/samn/vcsim/notebook.dol_1:24562)(notebook.dol_1:24492)
  cpercol[E2]  = 150 * scale
  cpercol[E4] =   30 * scale
  cpercol[E5B] =  int(17 * scale * E5BNumF)
  cpercol[E5R] =  int(65 * scale * E5RNumF)
  cpercol[E6] =   60 * scale
  cpercol[I2L] =  13 * scale
  cpercol[I2]  =  25 * scale
  cpercol[I4L] =  14 * scale 
  cpercol[I4]  =  20 * scale
  cpercol[I5L] =  13 * scale
  cpercol[I5]  =  25 * scale
  cpercol[I6L] =  13 * scale
  cpercol[I6] =   25 * scale
  cnt=allcells=icells=ecells=0
  for ct=0,CTYPi-1 if ((numc[ct]=cpercol[ct])>0) {
    ix[ct]=cnt ixe[ct]=cnt+numc[ct]-1 cnt+=numc[ct]
    if(ice(ct))icells+=numc[ct] else ecells+=numc[ct]
  } else numc[ct]=0
  allcells=ecells+icells
}
setcpercol()

//** pano2nq() reads in from a grvec panobj to an nq
// nq=pano2nq()
obfunc pano2nq () { local i,ii localobj st,oq,v1,xo
  oq=new NQS() st=new String2() v1=new Vector() i=0
  if (printlist.count>0) {
    for ({i=0 ii=0};ii<printlist.count-1;ii+=1) { xo=printlist.o(ii)
      if (strm(xo.name,"SPKS")) {
        sprint(st.s,"time%s",xo.name) sprint(st.t,"ind_%s",xo.name)
        oq.resize(st.s,st.t)
        oq.v[i]=xo.tvec oq.v[i+1]=xo.vec
        i+=2
      }
    }
  } else for panobj.rvtr(vec,&ii,"SPKS") {
    sprint(st.s,"time%s",panobj.tstr) sprint(st.t,"ind_%s",panobj.tstr)
    oq.resize(st.s,panobj.tvec,st.t,vec)
    i+=1
  }
  return oq
}

//** drlfp() 
proc drlfp () { local i,ii,beg,end localobj xo
  clrveclist() end=0 tmplist.remove_all()
  if (argtype(1)==1) panobj=$o1 
  if (numarg()==3) {beg=$2 end=$3}
  ge(0) i=gvmarkflag=0
  if (printlist.count>0) { for ii=0,printlist.count-1 { xo=printlist.o(ii)
    if (strm(xo.name,"LFP")) {
      tmplist.append(new String(xo.name))
      xo.vec.line(g,0.1,sg(printlist.count-ii+1).x,2)
    }
  }
  } else {
    for panobj.rvtr(vec,&ii,"LFP") {
      vec.add(ii*8e3)
      tmplist.append(new String(panobj.tstr))
      if (end>0) {
        savevec(vec.c(beg/0.1,vec.size()-(1000-end)/0.1)) // this is for tstop=1000 and vdt_LFP=0.1
      } else savevec(vec.c(50/0.1,vec.size-10)) // clip the edges
    }
    for ltrb(xo,veclist,&ii) { xo.line(g,0.1,sg(veclist.count-ii+1).x,2)}
  }
}

//** mkdrr() draw a graphic
decim=1e3 // decimate
proc mkdrr () { local n,i,j,k,ty localobj xq,v1
  gvmarkflag=1 ty=$1 lne=3 clr+=1 // ge(0) 
  xq=new NQS("t","ind") xq.verbose=0 v1=new Vector(decim)
  xq.marksym="O"
  for ({k=0 i=0 j=nq.m/2};i<nq.m/2;{i+=2 j+=2 k+=1}) for case(&x,i,j) { // print nq.s[x].s,k*1e3
    xq.v[0]=nq.v[x] xq.v[1]=nq.v[x+1]
    n=xq.select("ind","[]",ix[ty],ixe[ty])
    if (n>0) {
      if (decim>0 && decim<n) {  // decim will give final size for a group
        v1.resample(xq.out.v[1].c,decim/n) xq.out.v[1].copy(v1)
        v1.resample(xq.out.v[0].c,decim/n) xq.out.v[0].copy(v1)
      }
      xq.out.v[1].add(k*1.5e3) // for scale==2 (2*470)
      // print i,n,xq.getcol("i").min,xq.getcol("i").max
      xq.gr("ind","t",0,clr,lne)
    }
    k+=1
  }
  // drline(100,0,100,col.allcells*7,g,9,9)
}

proc drall () {
  if (argtype(1)==1) panobj=$o1
  {ge(0) clr=0  delnqs(nq) nq=pano2nq() mkdrr(E2) mkdrr(E4) mkdrr(E5B) mkdrr(E5R)}
  // drline(100,0,100,11e3,1,2,5)
}

//** svrun()
proc svrun () { local ii
  print output_file,comment
  panobj.pvplist(output_file,comment)
}


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