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 createSim(coil_center, coil_direction, dir_name, cpus=1):
# General Infoarmation
S = sim_struct.SESSION()
abPath = '/home/wq/下载/simnibs_examples/ernie/'
S.fnamehead = abPath + 'ernie.msh' # head mesh
S.pathfem = dir_name # Directory for the simulation
# 定义线圈类型
tms = S.add_tmslist()
tms.fnamecoil = 'Magstim_70mm_Fig8.nii.gz' # Choose a coil from the ccd-files folder
# 定义线圈位置
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(coil_center, abPath + 'm2m_ernie')
# Point the coil handle posteriorly, we just add 10 mm to the original M1 y coordinate
pos.pos_ydir = simnibs.mni2subject_coords(coil_direction, abPath + 'm2m_ernie')
pos.distance = 4 # 4 mm distance from coil surface to head surface
# Run Simulation
out = S.run(cpus, False, True)
re = simnibs.read_msh(S.pathfem + '/ernie_TMS_1-0001_Magstim_70mm_Fig8_nii_scalar.msh')
return re
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)
"""Script for simulating the TACS challenge montage. see @TACSchallenge on Twitter A. Thielscher, 2020 """ from copy import deepcopy from simnibs import sim_struct, run_simnibs ### general Information S = sim_struct.SESSION() S.fnamehead = 'ernie.msh' # head mesh S.pathfem = 'TACSchallenge' # Directory for the simulation S.map_to_surf = True S.open_in_gmsh = True # open results once they are ready # (set to False if you are annoyed by the popup windows) ### Define Condition A ConditionA = S.add_tdcslist() ### Set current flow though each channel: ### 2mA peak-to-peak --> 1 mA baseline-to-peak ### The third entry is a "pseudochannel" to which electrodes ### are connected that are not used in the simulated condition ConditionA.currents = [0.001, -0.001, 0.0] # Define occipital electrodes O1 = ConditionA.add_electrode() O1.channelnr = 1 # Connect the electrode to the first channel O1.centre = 'O1' # Place it over O1 O1.shape = 'ellipse' # Elliptical / circular shape
# In directory & files --> HARD CODED sub_dir = '/data/pt_neuam005/simnibs_TMS/subjects' coilnifti = '/data/pt_neuam005/simnibs_TMS/MagVenture_MC_B70.nii.gz' meshfile = os.path.join(sub_dir, sub, sub + '.msh') m2mfile = os.path.join(sub_dir, sub, 'm2m_' + sub) outfile = os.path.join(sub_dir, sub, 'simnibs_simulation') intFile = os.path.join(sub_dir, sub, 'tms_int_' + sub + '.txt') coordFile = os.path.join(sub_dir, sub, 'coordinates_' + sub + '.txt') tint = np.loadtxt(intFile).astype(float) coord = np.loadtxt(coordFile).astype(float)[1:].tolist()[0] # Initalize a session s = sim_struct.SESSION() s.fnamehead = meshfile s.subpath = m2mfile s.pathfem = outfile mesh = mesh_io.Msh(fn=s.fnamehead) # Initialize a list of TMS simulations tmslist = s.add_tmslist() tmslist.fnamecoil = coilnifti tmslist.anisotropy_type = 'scalar' # Initialize a TEMPORARY coil position to get params pos = tmslist.add_position() pos.centre = coord # entry coordinates
