from __future__ import print_function
import mne

from my_settings import * 

subject = sys.argv[1]

# make source space
src = mne.setup_source_space(subject, spacing='oct6',
                             subjects_dir=subjects_dir,
                             add_dist=False, overwrite=True)
# save source space
mne.write_source_spaces(mne_folder + "%s-oct6-src.fif" % subject, src)

conductivity = (0.3, 0.006, 0.3)  # for three layers
model = mne.make_bem_model(subject=subject, ico=None,
                           conductivity=conductivity,
                           subjects_dir=subjects_dir)
bem = mne.make_bem_solution(model)

mne.write_bem_solution(mne_folder + "%s-8194-bem-sol.fif" % subject)

from __future__ import print_function
import mne
import subprocess

from my_settings import * 

subject = sys.argv[1]

cmd = "/usr/local/common/meeg-cfin/configurations/bin/submit_to_isis"

# make source space
src = mne.setup_source_space(subject, spacing='oct6',
                             subjects_dir=subjects_dir,
                             add_dist=False, overwrite=True)
# save source space
mne.write_source_spaces(mne_folder + "%s-oct-6-src.fif" % subject, src)


setup_forward = "mne_setup_forward_model --subject %s --surf --ico -6" % (
    subject)
subprocess.call([cmd, "1", setup_forward])


# conductivity = (0.3, 0.006, 0.3)  # for three layers
# model = mne.make_bem_model(subject=subject, ico=None,
#                            conductivity=conductivity,
#                            subjects_dir=subjects_dir)
# bem = mne.make_bem_solution(model)

# mne.write_bem_solution(mne_folder + "%s-8194-bem-sol.fif" % subject)

Change to make BEM solution from mne-C
Change to make BEM solution from mne-C

  from __future__ import print_function
  import mne
+ import subprocess
  
  from my_settings import * 
  
  subject = sys.argv[1]
+ 
+ cmd = "/usr/local/common/meeg-cfin/configurations/bin/submit_to_isis"
  
  # make source space
  src = mne.setup_source_space(subject, spacing='oct6',
                               subjects_dir=subjects_dir,
                               add_dist=False, overwrite=True)
  # save source space
- mne.write_source_spaces(mne_folder + "%s-oct6-src.fif" % subject, src)
+ mne.write_source_spaces(mne_folder + "%s-oct-6-src.fif" % subject, src)
  
- conductivity = (0.3, 0.006, 0.3)  # for three layers
- model = mne.make_bem_model(subject=subject, ico=None,
-                            conductivity=conductivity,
-                            subjects_dir=subjects_dir)
- bem = mne.make_bem_solution(model)
  
- mne.write_bem_solution(mne_folder + "%s-8194-bem-sol.fif" % subject)
+ setup_forward = "mne_setup_forward_model --subject %s --surf --ico -6" % (
+     subject)
+ subprocess.call([cmd, "1", setup_forward])
  
+ 
+ # conductivity = (0.3, 0.006, 0.3)  # for three layers
+ # model = mne.make_bem_model(subject=subject, ico=None,
+ #                            conductivity=conductivity,
+ #                            subjects_dir=subjects_dir)
+ # bem = mne.make_bem_solution(model)
+ 
+ # mne.write_bem_solution(mne_folder + "%s-8194-bem-sol.fif" % subject)
+ 
Change to make BEM solution from mne-C
## Code Before:
from __future__ import print_function
import mne

from my_settings import * 

subject = sys.argv[1]

# make source space
src = mne.setup_source_space(subject, spacing='oct6',
                             subjects_dir=subjects_dir,
                             add_dist=False, overwrite=True)
# save source space
mne.write_source_spaces(mne_folder + "%s-oct6-src.fif" % subject, src)

conductivity = (0.3, 0.006, 0.3)  # for three layers
model = mne.make_bem_model(subject=subject, ico=None,
                           conductivity=conductivity,
                           subjects_dir=subjects_dir)
bem = mne.make_bem_solution(model)

mne.write_bem_solution(mne_folder + "%s-8194-bem-sol.fif" % subject)

## Instruction:
Change to make BEM solution from mne-C
## Code After:
from __future__ import print_function
import mne
import subprocess

from my_settings import * 

subject = sys.argv[1]

cmd = "/usr/local/common/meeg-cfin/configurations/bin/submit_to_isis"

# make source space
src = mne.setup_source_space(subject, spacing='oct6',
                             subjects_dir=subjects_dir,
                             add_dist=False, overwrite=True)
# save source space
mne.write_source_spaces(mne_folder + "%s-oct-6-src.fif" % subject, src)


setup_forward = "mne_setup_forward_model --subject %s --surf --ico -6" % (
    subject)
subprocess.call([cmd, "1", setup_forward])


# conductivity = (0.3, 0.006, 0.3)  # for three layers
# model = mne.make_bem_model(subject=subject, ico=None,
#                            conductivity=conductivity,
#                            subjects_dir=subjects_dir)
# bem = mne.make_bem_solution(model)

# mne.write_bem_solution(mne_folder + "%s-8194-bem-sol.fif" % subject)
