Problem in using TMS pulse (defined as tms2.mod) in netpyne

[Mohammadreza V.Farahani]

Hi everyone,

I am going to use a TMS pulse (defined as tms2.mod) in netpyne, but it's parameters seem unchangeable trough netParams.stimSourceParams.

I mean when I use below code to define a stimulation source, result do not change by changing it's parameters (for example 'onset')

netParams.stimSourceParams['Input_1'] = {'type': 'TMSpulse_bi','onset': 50, 'decay': 0.08, 'imax':40}

actually just below code is enough to make a stimulation

netParams.stimSourceParams['Input_1'] = {'type': 'TMSpulse_bi'}

would you please help me solve this issue and use  tms2.mod  in netpyne?

My operation system is Ms Widows 10 and I am using latest version of spyder(GUI), python, NetPyNE and Neuron. 

thanks

Source of  tms2.mod file: https://github.com/trieschlab/tms_model/tree/master/code/mechanisms

 tms2.mod as txt:

COMMENT
Monophasic current induced by a TMS stimulation. Positive values of i depolarize the cell.
ENDCOMMENT

NEURON {
POINT_PROCESS TMSpulse_bi
RANGE onset,decay,imax
ELECTRODE_CURRENT i
}

UNITS {
(nA) = (nanoamp)
(uS) = (microsiemens)
}

PARAMETER {
onset = 10 (ms)
decay = 0.08 (ms)
imax = 40 (nA)
}

ASSIGNED {
i (nA)
}

INITIAL {
i = 40 (nA)
}
BREAKPOINT {
if (imax) {
at_time(onset)
}

if ((t - onset) < 0 || (t - onset) > 20) {
i = 0
} else {
i = imax*sin (30*(t - onset)) * exp ( -(t - onset)/decay)
}


}

FUNCTION alpha(x) {
if (x < 0 || x > 20) {
alpha = 0
}else{
alpha = exp(1 - x) - x * exp(1 - x)
}
}

[Joe Graham]

Hello,

I'd be happy to take a look if you could include a minimal example that demonstrates the problem.  A simple sim with two cells with your stim mechanism set to different onset times which generates a plot of traces showing no change would do the job.

Cheers,

Joe

[Mohammadreza V.Farahani]

Dear Joe,

Thank you for your kind response

Blew is a simple sample that shows the problem. No matter which of highlighted lines is used, the result is the same. attachment include the code, .mod and .dll files.

 

from netpyne import specs, sim

# Network parameters

netParams = specs.NetParams()  # object of class NetParams to store the network parameters

## Cell types

PYRcell = {'secs': {}}

PYRcell['secs']['soma'] = {'geom': {}, 'mechs': {}}

PYRcell['secs']['soma']['geom'] = {'diam': 18.8, 'L': 18.8, 'Ra': 123.0}

PYRcell['secs']['soma']['mechs']['hh'] = {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70}

PYRcell['secs']['dend'] = {'geom': {}, 'topol': {}, 'mechs': {}}

PYRcell['secs']['dend']['geom'] = {'diam': 5.0, 'L': 150.0, 'Ra': 150.0, 'cm': 1}

PYRcell['secs']['dend']['topol'] = {'parentSec': 'soma', 'parentX': 1.0, 'childX': 0}

PYRcell['secs']['dend']['mechs']['pas'] = {'g': 0.0000357, 'e': -70}

netParams.cellParams['PYR'] = PYRcell

## Population parameters

netParams.popParams['S'] = {'cellType': 'PYR', 'numCells': 1}

netParams.popParams['M'] = {'cellType': 'PYR', 'numCells': 1}

## Synaptic mechanism parameters

netParams.synMechParams['exc'] = {'mod': 'Exp2Syn', 'tau1': 1.0, 'tau2': 5.0, 'e': 0}  # excitatory synaptic mechanism

# Stimulation parameters

netParams.stimSourceParams['Input_1'] = {'type': 'TMSpulse_bi'}

# netParams.stimSourceParams['Input_1'] = {'type': 'TMSpulse_bi','onset': 40, 'decay': 0.08, 'imax':40}

# netParams.stimSourceParams['Input_1'] = {'type': 'TMSpulse_bi','onset': 60, 'decay': 0.08, 'imax':40}

# netParams.stimSourceParams['Input_1'] = {'type': 'TMSpulse_bi','onset': 60, 'decay': 0.08, 'imax':10}

netParams.stimTargetParams['Input_1->S'] = {'source': 'Input_1', 'sec':'dend', 'loc': 0.5,'conds': {'pop':'S'}}

## Cell connectivity rules

netParams.connParams['S->M'] = {'preConds': {'pop': 'S'}, 'postConds': {'pop': 'M'},  #  S -> M

    'probability': 1,         # probability of connection

    'weight': 0.1,             # synaptic weight

    # 'delay': 5,                 # transmission delay (ms)

    'sec': 'dend',              # section to connect to

    'loc': 1.0,                 # location of synapse

    'synMech': 'exc'}           # target synaptic mechanism

# Simulation options

simConfig = specs.SimConfig()       # object of class SimConfig to store simulation configuration

simConfig.duration = 0.1*1e3        # Duration of the simulation, in ms

simConfig.dt = 0.025                # Internal integration timestep to use

simConfig.verbose = False           # Show detailed messages

simConfig.recordTraces = {'V_soma':{'sec':'soma','loc':0.5,'var':'v'}}  # Dict with traces to record

simConfig.recordStep = 0.1            # Step size in ms to save data (eg. V traces, LFP, etc)

simConfig.filename = 'test'         # Set file output name

simConfig.savePickle = False        # Save params, network and sim output to pickle file

simConfig.analysis['plotRaster'] = {'saveFig': True}                    # Plot a raster

simConfig.analysis['plotTraces'] = {'include': [0,1], 'saveFig': True}  # Plot recorded traces for this list of cells

simConfig.analysis['plot2Dnet'] = {'saveFig': True}                     # plot 2D cell positions and connections

# Create network and run simulation

sim.createSimulateAnalyze(netParams = netParams, simConfig = simConfig)

[Joe Graham]

Hello,

I had to do a little digging, but I figured out the problem.  While your mod file seems like a perfectly reasonable stimulation point process, it turns out that only builtin NEURON stimulation point processes can be specified using `stimSourceParams`.  The builtins: NetStim, IClamp, VClamp, SEClamp, and AlphaSynapse.

To use a point process other than those, you need to specify it in your cell model, rather than in stimSourceParams. I have attached a file showing how to do that, which does change the stim parameters.

It seems like NetPyNE should accept generic point process stimulations, so I have submitted a feature request: https://github.com/Neurosim-lab/netpyne/issues/637

It should be possible to set up a generic stimulation in a future NetPyNE release, but for now you can get the same results with the attached file.

Good luck, and don't hesitate to reach out.

Cheers,

Joe

[Mohammadreza V.Farahani]

Dear Joe,

Thank you very much. I learned a lot from the solution. I am looking forward to seeing the possibility to set up a generic stimulation in a future NetPyNE release.

[Joe Graham]

Hello,

Well, as it turns out, NetPyNE does already allow generic stimulations, but there was a bug in loading the exotic stimulation parameters/values.  I have fixed the bug, and your original model file runs correctly now (stim param values get changed as they should).

You can already use the updated code from our development branch (https://github.com/Neurosim-lab/netpyne/tree/development), or the fix will also be included in our next release, which should happen within a week.  

Best wishes,

Joe

[Mohammadreza V.Farahani]

Hello,

I suggest improving the netParams.stimSourceParams in the new update to accept stimulation time series instead of just one stimulation time. that will make netpyne very convenient to be used for modeling train of stimulation, which is used in rTMS and other repetitive stimulation technics.

Regards

Mohammadreza V.Farahani