def simulation(fnamehead,
pathfem,
pos_centre=[-74.296158, -10.213354, 28.307243],
pos_ydir=[-74.217369, -37.293205, 20.05232],
distance=4,
current_change=1e6):
# Initalize a session
s = sim_struct.SESSION()
# Name of head mesh
s.fnamehead = fnamehead
# Output folder
s.pathfem = pathfem
# Not to visualize results in gmsh when running simulations (else set to True)
s.open_in_gmsh = False
# Initialize a list of TMS simulations
tmslist = s.add_tmslist()
# Select coil. For full list of available coils, please see simnibs documentation
tmslist.fnamecoil = 'Magstim_70mm_Fig8.nii.gz'
# Initialize a coil position
pos = tmslist.add_position()
pos.centre = pos_centre # Place the coil over
pos.pos_ydir = pos_ydir # Point the coil towards
pos.distance = distance # Distance between coil and head
pos.didt = current_change # Rate of change of current in the coil, in A/s.
run_simnibs(s)
def run_simulation(self,
sim_output_name,
fnamecoil='MagVenture_MC_B70.ccd',
didt=1e6,
overwrite=False):
s = sim_struct.SESSION()
s.fnamehead = os.path.join(self.mesh_dir, self.subject + '.msh')
print('output dir: ', self.wf_base_dir)
try:
if overwrite and os.path.exists(os.path.join(
self.wf_base_dir), 'simnibs_simulations', sim_output_name):
os.rmdir(
os.path.join(self.wf_base_dir, 'simnibs_simulations',
sim_output_name))
os.makedirs(
os.path.join(self.wf_base_dir, 'simnibs_simulations',
sim_output_name))
except:
raise OSError(
'simulation directory exists, overwrite=True to overwrite the results!'
)
s.pathfem = os.path.join(self.wf_base_dir, 'simnibs_simulations',
sim_output_name)
s.map_to_vol = True
s.map_to_surf = True
tms = s.add_tmslist()
tms.fnamecoil = os.path.join(Simnibs.SIMNIBSDIR, 'simnibs',
'ccd-files', fnamecoil)
tms.add_positions_from_csv(
os.path.join(self.wf_base_dir, 'simnibs_targets', self.csv_fname))
for p in tms.pos:
p.didt = didt
run_simnibs(s)
Retcontr.thickness = [1.5, 1.5] ConditionA.electrode.append(deepcopy(Retcontr)) ConditionA.electrode[-1].centre = [-41.2, 78.8, -34.1] # coordinates determined in simnibs_gui # Define Condition B S.poslists.append(deepcopy(ConditionA)) ConditionB = S.poslists[-1] ConditionB.electrode[0].channelnr = 3 ConditionB.electrode[1].channelnr = 3 ConditionB.electrode[2].channelnr = 3 ConditionB.electrode[6].channelnr = 1 ConditionB.electrode[7].channelnr = 1 # Define Condition C S.poslists.append(deepcopy(ConditionA)) ConditionC = S.poslists[-1] ConditionC.electrode[0].channelnr = 2 ConditionC.electrode[1].channelnr = 1 ConditionC.electrode[2].channelnr = 2 ConditionC.electrode[3].channelnr = 3 ConditionC.electrode[4].channelnr = 3 ConditionC.electrode[5].channelnr = 3 ConditionC.electrode[6].channelnr = 3 ConditionC.electrode[7].channelnr = 3 run_simnibs(S)
''' Example of a SimNIBS tDCS leadfield in Python
Run with:
simnibs_python leadfield.py
Copyright (C) 2019 Guilherme B Saturnino
place script in the “ernie” folder of the example dataset
'''
from simnibs import sim_struct, run_simnibs
tdcs_lf = sim_struct.TDCSLEADFIELD()
# head mesh
tdcs_lf.fnamehead = 'ernie.msh'
# output directory
tdcs_lf.pathfem = 'leadfield'
# Uncoment to use the pardiso solver
#tdcs_lf.solver_options = 'pardiso'
# This solver is faster than the default. However, it requires much more
# memory (~12 GB)
run_simnibs(tdcs_lf)
Copyright (C) 2019 Guilherme B Saturnino ''' import simnibs # Initialize structure opt = simnibs.opt_struct.TDCSoptimize() # Select the leadfield file opt.leadfield_hdf = 'leadfield/ernie_leadfield_EEG10-10_UI_Jurak_2007.hdf5' # Select a name for the optimization opt.name = 'optimization/single_target' # Select a maximum total current (in A) opt.max_total_current = 2e-3 # Select a maximum current at each electrodes (in A) opt.max_individual_current = 1e-3 # Select a maximum number of active electrodes (optional) opt.max_active_electrodes = 8 # Define optimization target target = opt.add_target() # Position of target, in subject space! # please see tdcs_optimize_mni.py for how to use MNI coordinates target.positions = [-55.4, -20.7, 73.4] # Intensity of the electric field (in V/m) target.intensity = 0.2 # Run optimization simnibs.run_simnibs(opt)
def main():
args = parseArguments(sys.argv[1:])
run_simnibs(args.simnibs_file, args.cpus)
anode = tdcslist.add_electrode()
anode.channelnr = 1
anode.centre = 'C3'
anode.pos_ydir = 'C1'
anode.shape = 'rect'
anode.dimensions = [50, 50]
anode.thickness = 4
cathode = tdcslist.add_electrode()
cathode.channelnr = 2
cathode.centre = 'AF4'
cathode.pos_ydir = 'F6'
cathode.shape = 'rect'
cathode.dimensions = [50, 70]
cathode.thickness = 4
# Run the simulation in each subject
for sub in subjects:
# ALWAYS create a new SESSION when changing subjects
s = sim_struct.SESSION()
s.map_to_fsavg = True
s.fnamehead = os.path.join(sub, sub + '.msh')
s.pathfem = os.path.join(sub, 'bipolar')
# Don't open in gmsh
s.open_in_gmsh = False
# Add the tdcslist we defined above
s.add_poslist(tdcslist)
# Run the sumulation
run_simnibs(s)
pos.distance = 1. # coil distance (mm) pos.didt = tint * 1e6 # TMS intensity (A/s) pos.pos_ydir = ([1, 0, 0]) # coil towards right pos.calc_matsimnibs(mesh) # scalp projection pos.pos_ydir = (pos.matsimnibs[0:3, 3] + [1, 0, 0]).tolist() A = pos.centre B = pos.pos_ydir #### params needed !!! ################# HERE WE GO .... k = sim_struct.SESSION() k.fnamehead = meshfile k.subpath = m2mfile k.pathfem = outfile mylist = k.add_tmslist() mylist.fnamecoil = coilnifti mylist.anisotropy_type = 'scalar' POS = mylist.add_position() POS.centre = A # entry coordinates POS.distance = 1. # coil distance (mm) POS.didt = tint * 1e6 # TMS intensity (A/s) POS.pos_ydir = B k.open_in_gmsh = False k.map_to_vol = True k.map_to_MNI = True run_simnibs(k)
import simnibs from simnibs import sim_struct ### General Infoarmation S = sim_struct.SESSION() S.fnamehead = 'ernie.msh' # head mesh S.pathfem = 'tms_hand' # Directory for the simulation ## Define the TMS simulation tms = S.add_tmslist() tms.fnamecoil = 'Magstim_70mm_Fig8.nii.gz' # Choose a coil from the ccd-files folder # Define the coil position pos = tms.add_position() # Place coil over the hand knob # Here, the hand knob is defined in MNI coordinates (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034289/) # And transformed to subject coordinates # We can use positions in the cortex. SimNIBS will automatically project them to the skin surface # and add the specified distance pos.centre = simnibs.mni2subject_coords([-37, -21, 58], 'm2m_ernie') # Point the coil handle posteriorly, we just add 10 mm to the original M1 y coordinate pos.pos_ydir = simnibs.mni2subject_coords([-37, -21 - 10, 58], 'm2m_ernie') pos.distance = 4 # 4 mm distance from coil surface to head surface # Run Simulation simnibs.run_simnibs(S)
