def read_cmd_args(argv=None):
from src.utils import args_utils as au
import argparse
parser = argparse.ArgumentParser(description='MMVT electrodes preprocessing')
parser.add_argument('-s', '--subject', help='subject name', required=True, type=au.str_arr_type)
parser.add_argument('-t', '--task', help='task', required=False)
parser.add_argument('-a', '--atlas', help='atlas name', required=False, default='aparc.DKTatlas40')
parser.add_argument('-b', '--bipolar', help='bipolar', required=False, default=0, type=au.is_true)
parser.add_argument('-f', '--function', help='function name', required=False, default='all', type=au.str_arr_type)
parser.add_argument('--exclude', help='functions not to run', required=False, default='', type=au.str_arr_type)
parser.add_argument('--good_channels', help='good channels', required=False, default='', type=au.str_arr_type)
parser.add_argument('--bad_channels', help='bad channels', required=False, default='', type=au.str_arr_type)
parser.add_argument('--from_t', help='from_t', required=False, default=0, type=float) # was -500
parser.add_argument('--to_t', help='to_t', required=False, default=0, type=float) # was 2000
parser.add_argument('--from_t_ind', help='from_t_ind', required=False, default=0, type=int) # was -500
parser.add_argument('--to_t_ind', help='to_t_ind', required=False, default=-1, type=int) # was 2000
parser.add_argument('--indices_shift', help='indices_shift', required=False, default=0, type=int) # was 1000
parser.add_argument('--conditions', help='conditions', required=False, default='')
parser.add_argument('--raw_fname', help='raw fname', required=False, default='')
parser.add_argument('--stat', help='stat', required=False, default=STAT_DIFF, type=int)
parser.add_argument('--electrodes_names_field', help='electrodes_names_field', required=False, default='names')
parser.add_argument('--moving_average_window_size', help='', required=False, default=0, type=int)
parser.add_argument('--field_cond_template', help='', required=False, default='{}')
parser.add_argument('--input_type', help='', required=False, default='ERP')
parser.add_argument('--input_matlab_fname', help='', required=False, default='')
parser.add_argument('--ras_xls_sheet_name', help='ras_xls_sheet_name', required=False, default='')
parser.add_argument('--do_plot', help='do plot', required=False, default=0, type=au.is_true)
args = utils.Bag(au.parse_parser(parser, argv))
print(args)
return args
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('--python_cmd',
help='python cmd',
required=False,
default=sys.executable)
return su.Bag(au.parse_parser(parser, argv))
def read_cmd_args(argv=None):
import argparse
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='MMVT stim preprocessing')
parser.add_argument('-c', '--conditions', help='conditions names', required=False, default='contrast', type=au.str_arr_type)
parser.add_argument('--mat_fname', help='matlab connection file name', required=False, default='')
parser.add_argument('--mat_field', help='matlab connection field name', required=False, default='')
parser.add_argument('--labels_exclude', help='rois to exclude', required=False, default='unknown,corpuscallosum',
type=au.str_arr_type)
parser.add_argument('--bipolar', help='', required=False, default=0, type=au.is_true)
parser.add_argument('--norm_by_percentile', help='', required=False, default=1, type=au.is_true)
parser.add_argument('--norm_percs', help='', required=False, default='1,99', type=au.int_arr_type)
parser.add_argument('--stat', help='', required=False, default=STAT_DIFF, type=int)
parser.add_argument('--windows', help='', required=False, default=0, type=int)
parser.add_argument('--t_max', help='', required=False, default=0, type=int)
parser.add_argument('--threshold_percentile', help='', required=False, default=0, type=int)
parser.add_argument('--threshold', help='', required=False, default=0, type=float)
parser.add_argument('--color_map', help='', required=False, default='jet')
parser.add_argument('--symetric_colors', help='', required=False, default=1, type=au.is_true)
parser.add_argument('--data_max', help='', required=False, default=0, type=float)
parser.add_argument('--data_min', help='', required=False, default=0, type=float)
pu.add_common_args(parser)
args = utils.Bag(au.parse_parser(parser, argv))
if len(args.conditions) == 1:
args.stat = STAT_AVG
print(args)
return args
def read_cmd_args(argv=None):
import argparse
parser = argparse.ArgumentParser(description='MMVT anatomy preprocessing')
parser.add_argument('--template_subject', help='template subject', required=False, default='fsaverage')
parser.add_argument('--surf_name', help='surf_name', required=False, default='pial')
parser.add_argument('--cerebellum_segmentation_loose', help='', required=False, default=1, type=au.is_true)
parser.add_argument('--overwrite', help='overwrite', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_subcorticals', help='overwrite', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_annotation', help='overwrite_annotation', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_morphing_labels', help='overwrite_morphing_labels', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_hemis_srf', help='overwrite_hemis_srf', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_labels_ply_files', help='overwrite_labels_ply_files', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_faces_verts', help='overwrite_faces_verts', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_ply_files', help='overwrite_ply_files', required=False, default=0, type=au.is_true)
parser.add_argument('--solve_labels_collisions', help='solve_labels_collisions', required=False, default=0, type=au.is_true)
parser.add_argument('--morph_labels_from_fsaverage', help='morph_labels_from_fsaverage', required=False, default=1, type=au.is_true)
parser.add_argument('--fs_labels_fol', help='fs_labels_fol', required=False, default='')
pu.add_common_args(parser)
args = utils.Bag(au.parse_parser(parser, argv))
args.necessary_files = {'mri': ['aseg.mgz', 'norm.mgz', 'ribbon.mgz', 'T1.mgz', 'orig.mgz'],
'surf': ['rh.pial', 'lh.pial', 'rh.inflated', 'lh.inflated', 'lh.curv', 'rh.curv', 'rh.sphere.reg',
'lh.sphere.reg', 'lh.white', 'rh.white', 'rh.smoothwm','lh.smoothwm'],
'mri:transforms' : ['talairach.xfm']}
if args.overwrite:
args.overwrite_annotation = True
args.overwrite_morphing_labels = True
args.overwrite_hemis_srf = True
args.overwrite_labels_ply_files = True
args.overwrite_faces_verts = True
args.overwrite_fs_files = True
print(args)
return args
def read_cmd_args(argv=None):
import argparse
parser = argparse.ArgumentParser(description='UDP listener')
parser.add_argument('-b', '--buffer_size', required=False, default=10, type=int)
# parser.add_argument('-p', '--python_cmd', required=False, default='python')
# parser.add_argument('-f', '--function', required=False, default='')
return utils.Bag(au.parse_parser(parser, argv))
def read_cmd_args(argv):
import argparse
parser = argparse.ArgumentParser(description='MMVT freeview preprocessing')
parser.add_argument('-b',
'--bipolar',
help='bipolar',
required=False,
default=0,
type=au.is_true)
parser.add_argument('--overwrite_aseg_file',
help='overwrite_aseg_file',
required=False,
default=0,
type=au.is_true)
parser.add_argument('--create_volume_file',
help='create_volume_file',
required=False,
default=1,
type=au.is_true)
parser.add_argument('--electrodes_pos_fname',
help='electrodes_pos_fname',
required=False,
default='')
parser.add_argument('--way_points',
help='way_points',
required=False,
default=0,
type=au.is_true)
pu.add_common_args(parser)
args = utils.Bag(au.parse_parser(parser, argv))
args.necessary_files = {'mri': ['T1.mgz', 'orig.mgz']}
# print(args)
return args
def read_cmd_args(argv=None):
import argparse
parser = argparse.ArgumentParser(description='MMVT template preprocessing')
parser.add_argument('--flag', help='', required=False, default='')
pu.add_common_args(parser)
args = utils.Bag(au.parse_parser(parser, argv))
return args
def read_cmd_args(argv=None):
import argparse
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='MMVT template preprocessing')
pu.add_common_args(parser)
args = utils.Bag(au.parse_parser(parser))
# print(args)
return args
def parse_args(parser, argv, raise_exception_if_subject_is_empty=True):
args = Bag(au.parse_parser(parser, argv))
args.real_atlas = get_real_atlas_name(args.atlas)
if ((len(args.subjects) == 0 and args.subject == '') or (len(args.subjects) > 0 and args.subject != '')) and \
raise_exception_if_subject_is_empty:
# print(args)
raise Exception('You need to set --subject or --subjects!')
return args
def read_cmd_args(argv=None):
import argparse
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='MMVT template preprocessing')
pu.add_common_args(parser)
args = utils.Bag(au.parse_parser(parser))
print(args)
return args
def parse_args(parser, argv):
args = Bag(au.parse_parser(parser, argv))
args.real_atlas = get_full_atlas_name(args.atlas)
if (len(args.subjects) == 0
and args.subject == '') or (len(args.subjects) > 0
and args.subject != ''):
raise Exception('You need to set --subject or --subjects!')
return args
def read_cmd_args(argv=None):
import argparse
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='Description of your program')
parser.add_argument('-s', '--subject', help='subject name', required=True)
parser.add_argument('-f',
'--function',
help='function name',
required=False,
default='all')
parser.add_argument('-c',
'--contrast',
help='contrast name',
required=True)
parser.add_argument('-a',
'--atlas',
help='atlas name',
required=False,
default='aparc.DKTatlas40')
parser.add_argument('-t',
'--threshold',
help='clustering threshold',
required=False,
default='2')
parser.add_argument('-T', '--task', help='task', required=True)
parser.add_argument('--existing_format',
help='existing format',
required=False,
default='mgz')
parser.add_argument('--volume_type',
help='volume type',
required=False,
default='mni305')
parser.add_argument('--volume_name',
help='volume file name',
required=False,
default='')
parser.add_argument('--surface_name',
help='surface_name',
required=False,
default='pial')
parser.add_argument('--meg_subject',
help='meg_subject',
required=False,
default='')
parser.add_argument('--inverse_method',
help='inverse method',
required=False,
default='dSPM')
parser.add_argument('--n_jobs', help='cpu num', required=False, default=-1)
args = utils.Bag(au.parse_parser(parser, argv))
args.n_jobs = utils.get_n_jobs(args.n_jobs)
print(args)
return args
def read_cmd_args(argv):
import argparse
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='MMVT freeview preprocessing')
parser.add_argument('-b', '--bipolar', help='bipolar', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_aseg_file', help='overwrite_aseg_file', required=False, default=0, type=au.is_true)
parser.add_argument('--create_volume_file', help='create_volume_file', required=False, default=1, type=au.is_true)
parser.add_argument('--electrodes_pos_fname', help='electrodes_pos_fname', required=False, default='')
parser.add_argument('--way_points', help='way_points', required=False, default=0, type=au.is_true)
pu.add_common_args(parser)
args = utils.Bag(au.parse_parser(parser, argv))
args.necessary_files = {'mri': ['T1.mgz', 'orig.mgz']}
print(args)
return args
def read_cmd_args(argv=None):
import argparse
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='MMVT stim preprocessing')
parser.add_argument('--stim_channel', help='stim channel', required=True)
parser.add_argument('--colors_map', help='activity colors map', required=False, default='OrRd')
parser.add_argument('--norm_percs', help='normalization percerntiles', required=False, type=au.int_arr_type, default='1,95')
parser.add_argument('--downsample', help='downsample', required=False, type=int, default=1)
parser.add_argument('--file_frefix', help='file_frefix', required=False, default='psd_')
parser.add_argument('--error_radius', help='error_radius', required=False, default=3, type=int)
parser.add_argument('--elec_length', help='elec_length', required=False, default=4, type=int)
pu.add_common_args(parser)
args = utils.Bag(au.parse_parser(parser))
print(args)
return args
def main():
import collections
parser = argparse.ArgumentParser(description='MMVT')
parser.add_argument('-s', '--subject', help='subject name', required=True, type=au.str_arr_type)
parser.add_argument('-a', '--atlas', help='atlas name', required=False, default='aparc.DKTatlas')
parser.add_argument('-u', '--sftp_username', help='sftp username', required=False, default='npeled')
parser.add_argument('-d', '--sftp_domain', help='sftp domain', required=False, default='door.nmr.mgh.harvard.edu')
parser.add_argument('--remote_subject_dir', help='remote_subjects_dir', required=False,
default='/space/thibault/1/users/npeled/subjects/{subject}')
parser.add_argument('-f', '--function', help='function name', required=True)
# choices=[f_name for f_name, f in globals().items() if isinstance(f, collections.Callable)
# if f_name not in ['Gooey', 'main']]
args = utils.Bag(au.parse_parser(parser))
# for subject in args.subject:
globals()[args.function](args)
def read_cmd_args(argv=None):
import argparse
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='MMVT anatomy preprocessing')
parser.add_argument('-s', '--subject', help='subject name', required=True, type=au.str_arr_type)
parser.add_argument('-a', '--atlas', help='atlas name', required=False, default='aparc.DKTatlas40')
parser.add_argument('-f', '--function', help='functions to run', required=False, default='all', type=au.str_arr_type)
parser.add_argument('--exclude', help='functions not to run', required=False, default='', type=au.str_arr_type)
parser.add_argument('--ignore_missing', help='ignore missing files', required=False, default=0, type=au.is_true)
parser.add_argument('--fsaverage', help='fsaverage', required=False, default='fsaverage')
parser.add_argument('--remote_subject_dir', help='remote_subject_dir', required=False, default='')
parser.add_argument('--surf_name', help='surf_name', required=False, default='pial')
parser.add_argument('--overwrite', help='overwrite', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_fs_files', help='overwrite freesurfer files', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_annotation', help='overwrite_annotation', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_morphing_labels', help='overwrite_morphing_labels', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_hemis_srf', help='overwrite_hemis_srf', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_labels_ply_files', help='overwrite_labels_ply_files', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_faces_verts', help='overwrite_faces_verts', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_ply_files', help='overwrite_ply_files', required=False, default=0, type=au.is_true)
parser.add_argument('--solve_labels_collisions', help='solve_labels_collisions', required=False, default=0, type=au.is_true)
parser.add_argument('--morph_labels_from_fsaverage', help='morph_labels_from_fsaverage', required=False, default=1, type=au.is_true)
parser.add_argument('--fs_labels_fol', help='fs_labels_fol', required=False, default='')
parser.add_argument('--sftp', help='copy subjects files over sftp', required=False, default=0, type=au.is_true)
parser.add_argument('--sftp_username', help='sftp username', required=False, default='')
parser.add_argument('--sftp_domain', help='sftp domain', required=False, default='')
parser.add_argument('--print_traceback', help='print_traceback', required=False, default=1, type=au.is_true)
parser.add_argument('--n_jobs', help='cpu num', required=False, default=-1)
args = utils.Bag(au.parse_parser(parser, argv))
args.necessary_files = {'mri': ['aseg.mgz', 'norm.mgz', 'ribbon.mgz', 'T1.mgz'],
'surf': ['rh.pial', 'lh.pial', 'rh.inflated', 'lh.inflated', 'lh.curv', 'rh.curv', 'rh.sphere.reg', 'lh.sphere.reg', 'lh.white', 'rh.white', 'rh.smoothwm','lh.smoothwm'],
'mri:transforms' : ['talairach.xfm']}
args.n_jobs = utils.get_n_jobs(args.n_jobs)
if args.overwrite:
args.overwrite_annotation = True
args.overwrite_morphing_labels = True
args.overwrite_hemis_srf = True
args.overwrite_labels_ply_files = True
args.overwrite_faces_verts = True
args.overwrite_fs_files = True
print(args)
return args
def read_cmd_args(argv=None):
import argparse
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='MMVT anatomy preprocessing')
parser.add_argument('-s', '--subject', help='subject name', required=True, type=au.str_arr_type)
parser.add_argument('-a', '--atlas', help='atlas name', required=False, default='aparc.DKTatlas40')
parser.add_argument('-f', '--function', help='functions to run', required=False, default='all', type=au.str_arr_type)
parser.add_argument('--exclude', help='functions not to run', required=False, default='', type=au.str_arr_type)
parser.add_argument('--ignore_missing', help='ignore missing files', required=False, default=0, type=au.is_true)
parser.add_argument('--fsaverage', help='fsaverage', required=False, default='fsaverage')
parser.add_argument('--remote_subject_dir', help='remote_subject_dir', required=False, default='')
parser.add_argument('--remote_subjects_dir', help='remote_subjects_dir', required=False, default='')
parser.add_argument('--surf_name', help='surf_name', required=False, default='pial')
parser.add_argument('--overwrite', help='overwrite', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_fs_files', help='overwrite freesurfer files', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_annotation', help='overwrite_annotation', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_morphing_labels', help='overwrite_morphing_labels', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_hemis_srf', help='overwrite_hemis_srf', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_labels_ply_files', help='overwrite_labels_ply_files', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_faces_verts', help='overwrite_faces_verts', required=False, default=0, type=au.is_true)
parser.add_argument('--overwrite_ply_files', help='overwrite_ply_files', required=False, default=0, type=au.is_true)
parser.add_argument('--solve_labels_collisions', help='solve_labels_collisions', required=False, default=0, type=au.is_true)
parser.add_argument('--morph_labels_from_fsaverage', help='morph_labels_from_fsaverage', required=False, default=1, type=au.is_true)
parser.add_argument('--fs_labels_fol', help='fs_labels_fol', required=False, default='')
parser.add_argument('--sftp', help='copy subjects files over sftp', required=False, default=0, type=au.is_true)
parser.add_argument('--sftp_username', help='sftp username', required=False, default='')
parser.add_argument('--sftp_domain', help='sftp domain', required=False, default='')
parser.add_argument('--print_traceback', help='print_traceback', required=False, default=1, type=au.is_true)
parser.add_argument('--n_jobs', help='cpu num', required=False, default=-1)
args = utils.Bag(au.parse_parser(parser, argv))
args.necessary_files = {'mri': ['aseg.mgz', 'norm.mgz', 'ribbon.mgz'],
'surf': ['rh.pial', 'lh.pial', 'rh.sphere.reg', 'lh.sphere.reg', 'lh.white', 'rh.white', 'rh.smoothwm','lh.smoothwm']}
args.n_jobs = utils.get_n_jobs(args.n_jobs)
if args.overwrite:
args.overwrite_annotation = True
args.overwrite_morphing_labels = True
args.overwrite_hemis_srf = True
args.overwrite_labels_ply_files = True
args.overwrite_faces_verts = True
args.overwrite_fs_files = True
print(args)
return args
def main():
import argparse
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='MMVT Setup')
parser.add_argument('-l', '--links', help='links folder name', required=False, default='links')
parser.add_argument('-g', '--gui', help='choose folders using gui', required=False, default='1', type=au.is_true)
args = utils.Bag(au.parse_parser(parser))
links_created = create_links(args.links, args.gui)
if not links_created:
print('Not all the links were created! Make sure all the links are created before running MMVT.')
else:
links_dir = utils.get_links_dir()
mmvt_root_dir = op.join(links_dir, 'mmvt')
resource_file_exist = copy_resources_files(mmvt_root_dir)
if not resource_file_exist:
print('Not all the resources files were copied to the MMVT () folder.\n'.format(mmvt_root_dir) +
'Please copy them manually from the mmvt_code/resources folder')
else:
print('Finish!')
def read_cmd_args(argv=None):
from src.utils import args_utils as au
import argparse
parser = argparse.ArgumentParser(description='MMVT electrodes preprocessing')
parser.add_argument('-b', '--bipolar', help='bipolar', required=False, default=0, type=au.is_true)
parser.add_argument('--good_channels', help='good channels', required=False, default='', type=au.str_arr_type)
parser.add_argument('--bad_channels', help='bad channels', required=False, default='', type=au.str_arr_type)
parser.add_argument('--from_t', help='from_t', required=False, default='0', type=au.float_arr_type)# float) # was -500
parser.add_argument('--to_t', help='to_t', required=False, default='0', type=au.float_arr_type) # was 2000
parser.add_argument('--from_t_ind', help='from_t_ind', required=False, default=0, type=int) # was -500
parser.add_argument('--to_t_ind', help='to_t_ind', required=False, default=-1, type=int) # was 2000
parser.add_argument('--indices_shift', help='indices_shift', required=False, default=0, type=int) # was 1000
parser.add_argument('--conditions', help='conditions', required=False, default='')
parser.add_argument('--raw_fname', help='raw fname', required=False, default='no_raw_fname_given')
parser.add_argument('--ref_elec', help='referece electrode', required=False, default='')
parser.add_argument('--stat', help='stat', required=False, default=STAT_DIFF, type=int)
parser.add_argument('--electrodes_names_field', help='electrodes_names_field', required=False, default='names')
parser.add_argument('--moving_average_window_size', help='', required=False, default=0, type=int)
parser.add_argument('--field_cond_template', help='', required=False, default='{}')
parser.add_argument('--input_type', help='', required=False, default='ERP')
parser.add_argument('--input_matlab_fname', help='', required=False, default='')
parser.add_argument('--start_time', help='', required=False, default='')
parser.add_argument('--seizure_time', help='', required=False, default='')
parser.add_argument('--window_length', help='', required=False, default=0, type=float)
parser.add_argument('--seizure_onset_time', help='', required=False, default=0, type=float)
parser.add_argument('--baseline_delta', help='', required=False, default=0, type=float)
parser.add_argument('--time_format', help='', required=False, default='%H:%M:%S')
parser.add_argument('--electrodes_groups_coloring_fname', help='', required=False, default='electrodes_groups_coloring.csv')
parser.add_argument('--ras_xls_sheet_name', help='ras_xls_sheet_name', required=False, default='')
parser.add_argument('--do_plot', help='do plot', required=False, default=0, type=au.is_true)
pu.add_common_args(parser)
args = utils.Bag(au.parse_parser(parser, argv))
args.ignore_missing = True
for field in ['from_t', 'to_t']:
if len(args[field]) == 1:
args[field] = args[field][0]
args.necessary_files = {'electrodes': ['{subject}_RAS.csv']}
print(args)
return args
def read_cmd_args(argv):
import argparse
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='MMVT freeview preprocessing')
parser.add_argument('-s', '--subject', help='subject name', required=True, type=au.str_arr_type)
parser.add_argument('-a', '--atlas', help='atlas name', required=False, default='aparc.DKTatlas40')
parser.add_argument('-b', '--bipolar', help='bipolar', required=False, default=0, type=bool)
parser.add_argument('-f', '--function', help='function name', required=False, default='all', type=au.str_arr_type)
parser.add_argument('--overwrite_aseg_file', help='overwrite_aseg_file', required=False, default=0, type=au.is_true)
parser.add_argument('--create_volume_file', help='create_volume_file', required=False, default=1, type=au.is_true)
parser.add_argument('--electrodes_pos_fname', help='electrodes_pos_fname', required=False, default='')
parser.add_argument('--way_points', help='way_points', required=False, default=0, type=au.is_true)
parser.add_argument('--remote_subject_dir', help='remote_subject_dir', required=False, default='')
parser.add_argument('--overwrite_fs_files', help='overwrite freesurfer files', required=False, default=0, type=au.is_true)
parser.add_argument('--sftp', help='copy subjects files over sftp', required=False, default=0, type=au.is_true)
parser.add_argument('--sftp_username', help='sftp username', required=False, default='')
parser.add_argument('--sftp_domain', help='sftp domain', required=False, default='')
parser.add_argument('--print_traceback', help='print_traceback', required=False, default=1, type=au.is_true)
args = utils.Bag(au.parse_parser(parser, argv))
args.necessary_files = {'mri': ['T1.mgz', 'orig.mgz']}
print(args)
return args
def read_cmd_args(argv=None):
import argparse
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='Description of your program')
parser.add_argument('-s', '--subject', help='subject name', required=True)
parser.add_argument('-f', '--function', help='function name', required=False, default='all')
parser.add_argument('-c', '--contrast', help='contrast name', required=True)
parser.add_argument('-a', '--atlas', help='atlas name', required=False, default='aparc.DKTatlas40')
parser.add_argument('-t', '--threshold', help='clustering threshold', required=False, default='2')
parser.add_argument('-T', '--task', help='task', required=True)
parser.add_argument('--existing_format', help='existing format', required=False, default='mgz')
parser.add_argument('--volume_type', help='volume type', required=False, default='mni305')
parser.add_argument('--volume_name', help='volume file name', required=False, default='')
parser.add_argument('--surface_name', help='surface_name', required=False, default='pial')
parser.add_argument('--meg_subject', help='meg_subject', required=False, default='')
parser.add_argument('--inverse_method', help='inverse method', required=False, default='dSPM')
parser.add_argument('--n_jobs', help='cpu num', required=False, default=-1)
args = utils.Bag(au.parse_parser(parser, argv))
args.n_jobs = utils.get_n_jobs(args.n_jobs)
print(args)
return args
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('--python_cmd', help='python cmd', required=False, default=sys.executable)
return su.Bag(au.parse_parser(parser, argv))
def read_cmd_args(argv=None):
import argparse
parser = argparse.ArgumentParser(description='MMVT CT preprocessing')
parser.add_argument('--ct_raw_input_fol',
help='',
required=False,
default='')
parser.add_argument('--ct_fol', help='', required=False, default='')
parser.add_argument('--ct_org_name',
help='',
required=False,
default='ct_org.mgz')
parser.add_argument('--nnv_ct_name',
help='',
required=False,
default='ct_no_large_negative_values.mgz')
parser.add_argument('--register_ct_name',
help='',
required=False,
default='ct_reg_to_mr.mgz')
parser.add_argument('--negative_threshold',
help='',
required=False,
default=-200,
type=int)
parser.add_argument('--no_negatives',
help='',
required=False,
default=True,
type=au.is_true)
parser.add_argument('--register_cost_function',
help='',
required=False,
default='nmi')
parser.add_argument('--ct_threshold',
help='',
required=False,
type=float,
default=2000)
parser.add_argument('--overwrite',
help='',
required=False,
default=0,
type=au.is_true)
parser.add_argument('--print_only',
help='',
required=False,
default=False,
type=au.is_true)
parser.add_argument('--ask_before',
help='',
required=False,
default=False,
type=au.is_true)
parser.add_argument('--debug',
help='',
required=False,
default=False,
type=au.is_true)
# find_electrodes:
parser.add_argument('--n_components',
help='',
required=False,
default=0,
type=int)
parser.add_argument('--n_groups',
help='',
required=False,
default=0,
type=int)
parser.add_argument('--brain_mask_fname',
help='',
required=False,
default='')
parser.add_argument('--output_fol',
help='',
required=False,
default=None,
type=au.str_or_none)
parser.add_argument('--clustering_method',
help='',
required=False,
default='knn')
parser.add_argument('--max_iters',
help='',
required=False,
default=5,
type=int)
parser.add_argument('--cylinder_error_radius',
help='',
required=False,
default=3,
type=float)
parser.add_argument('--min_elcs_for_lead',
help='',
required=False,
default=4,
type=int)
parser.add_argument('--max_dist_between_electrodes',
help='',
required=False,
default=20,
type=float)
parser.add_argument('--min_cylinders_ang',
help='',
required=False,
default=0.1,
type=float)
parser.add_argument('--ct_thresholds',
help='',
required=False,
default='99,99.9,99.95,99.99,99.995,99.999',
type=au.float_arr_type)
parser.add_argument('--min_joined_items_num',
help='',
required=False,
default=1,
type=int)
parser.add_argument('--min_distance_beteen_electrodes',
help='',
required=False,
default=2,
type=float)
# Dell
parser.add_argument('--voxels',
help='',
required=False,
default='',
type=au.list_of_int_lists_type)
parser.add_argument('--voxel',
help='',
required=False,
default='',
type=au.int_arr_type) # 102,99,131
parser.add_argument('--pixels_around_voxel',
help='',
required=False,
default=30,
type=int)
parser.add_argument('--interactive',
help='',
required=False,
default=0,
type=au.is_true)
parser.add_argument('--electrodes_names',
help='',
required=False,
default='',
type=au.str_arr_type)
parser.add_argument('--group_name', help='', required=False, default='')
parser.add_argument('--elc_name', help='', required=False, default='')
parser.add_argument('--fig_name', help='', required=False, default='')
parser.add_argument('--isotropization_type',
help='',
required=False,
default=1,
type=int)
pu.add_common_args(parser)
args = utils.Bag(au.parse_parser(parser, argv))
pu.set_default_folders(args)
args.necessary_files = {'mri': ['brain.mgz']}
global SUBJECTS_DIR, MMVT_DIR
SUBJECTS_DIR = args.mri_dir
MMVT_DIR = args.mmvt_dir
print('Subjects dir: {}'.format(SUBJECTS_DIR))
print('MMVT dir: {}'.format(MMVT_DIR))
return args
args.mat_field = 'figure_file'
args.windows = 1
args.stat = con.STAT_DIFF
args.threshold_percentile = 99
args.conditions = ['task', 'rest']
con.save_rois_connectivity(subject, args)
def example2(subject):
# subject = 'fsaverage5c'
args = con.read_cmd_args(['-s', subject])
args.atlas = 'laus125'
args.mat_fname = '/cluster/neuromind/npeled/linda/figure_file3.mat'
args.mat_field = 'matrix_cognition_ratio_fpn_dmn'
args.windows = 1
args.threshold = 0
args.norm_by_percentile = False
args.symetric_colors = False
args.color_map = 'YlOrRd'
args.data_min = 0.15
args.data_max = 0.6
con.save_rois_connectivity(subject, args)
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='MMVT')
parser.add_argument('-s', '--subject', help='subject name', required=True, type=au.str_arr_type)
parser.add_argument('-f', '--function', help='function name', required=True)
args = utils.Bag(au.parse_parser(parser))
for subject in args.subject:
locals()[args.function](subject)
def read_cmd_args(argv):
import argparse
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='MMVT freeview preprocessing')
parser.add_argument('-s',
'--subject',
help='subject name',
required=True,
type=au.str_arr_type)
parser.add_argument('-a',
'--atlas',
help='atlas name',
required=False,
default='aparc.DKTatlas40')
parser.add_argument('-b',
'--bipolar',
help='bipolar',
required=False,
default=0,
type=au.is_true)
parser.add_argument('-f',
'--function',
help='function name',
required=False,
default='all',
type=au.str_arr_type)
parser.add_argument('--overwrite_aseg_file',
help='overwrite_aseg_file',
required=False,
default=0,
type=au.is_true)
parser.add_argument('--create_volume_file',
help='create_volume_file',
required=False,
default=1,
type=au.is_true)
parser.add_argument('--electrodes_pos_fname',
help='electrodes_pos_fname',
required=False,
default='')
parser.add_argument('--way_points',
help='way_points',
required=False,
default=0,
type=au.is_true)
parser.add_argument('--remote_subject_dir',
help='remote_subject_dir',
required=False,
default='')
parser.add_argument('--overwrite_fs_files',
help='overwrite freesurfer files',
required=False,
default=0,
type=au.is_true)
parser.add_argument('--sftp',
help='copy subjects files over sftp',
required=False,
default=0,
type=au.is_true)
parser.add_argument('--sftp_username',
help='sftp username',
required=False,
default='')
parser.add_argument('--sftp_domain',
help='sftp domain',
required=False,
default='')
parser.add_argument('--print_traceback',
help='print_traceback',
required=False,
default=1,
type=au.is_true)
args = utils.Bag(au.parse_parser(parser, argv))
args.necessary_files = {'mri': ['T1.mgz', 'orig.mgz']}
print(args)
return args
return atlas in ['aparc.DKTatlas40', 'aparc', 'aparc.a2009s']
def read_surface(subject, subjects_dir, surf_type='pial'):
verts, faces = {}, {}
for hemi in utils.HEMIS:
surf_fname = op.join(subjects_dir, subject, 'surf',
'{}.{}'.format(hemi, surf_type))
if not op.isfile(surf_fname):
print('{} does not exist!'.format(surf_fname))
return None, None
verts[hemi], faces[hemi] = nib.freesurfer.read_geometry(surf_fname)
return verts, faces
if __name__ == '__main__':
import argparse
from src.utils.utils import Bag
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='MMVT')
parser.add_argument('-s', '--subject', help='subject name', required=True)
parser.add_argument('-f',
'--function',
help='function name',
required=True,
type=au.str_arr_type)
args = Bag(au.parse_parser(parser))
for func in args.function:
locals()[func](**args)
def main():
import collections
parser = argparse.ArgumentParser(description='MMVT')
parser.add_argument('-s',
'--subject',
help='subject name',
required=True,
type=au.str_arr_type)
parser.add_argument('-a',
'--atlas',
help='atlas name',
required=False,
default='aparc.DKTatlas')
parser.add_argument('-u',
'--sftp_username',
help='sftp username',
required=False,
default='npeled')
parser.add_argument('-d',
'--sftp_domain',
help='sftp domain',
required=False,
default='door.nmr.mgh.harvard.edu')
parser.add_argument(
'--remote_subject_dir',
help='remote_subjects_dir',
required=False,
default='/space/thibault/1/users/npeled/subjects/{subject}')
parser.add_argument(
'--fs_root',
help='freesurfer_root',
required=False,
default='/space/megraid/clinical/MEG-MRI/seder/freesurfer')
parser.add_argument('--dicoms_root',
help='dicoms_root',
required=False,
default='/cluster/archive/331/siemens')
parser.add_argument('--dicoms_fol',
help='dicoms_fol',
required=False,
default='',
type=au.str_arr_type)
parser.add_argument('--clin_fol',
help='clin_fol',
required=False,
default='',
type=au.str_arr_type)
parser.add_argument('--clin_root',
help='clin_fol',
required=False,
default='/space/megraid/clinical/MEG-MRI/')
parser.add_argument('--print_only',
help='',
required=False,
default=0,
type=au.is_true)
parser.add_argument('-f',
'--function',
help='function name',
required=True)
parser.add_argument('--n_jobs',
help='jobs num',
required=False,
default=4,
type=int)
# choices=[f_name for f_name, f in globals().items() if isinstance(f, collections.Callable)
# if f_name not in ['Gooey', 'main']]
args = utils.Bag(au.parse_parser(parser))
# for subject in args.subject:
globals()[args.function](args)
def read_cmd_args(argv=None):
import argparse
from src.utils import args_utils as au
parser = argparse.ArgumentParser(description='MMVT stim preprocessing')
parser.add_argument('-s',
'--subject',
help='subject name',
required=True,
type=au.str_arr_type)
parser.add_argument('-c',
'--conditions',
help='conditions names',
required=False,
default='contrast',
type=au.str_arr_type)
parser.add_argument('-a',
'--atlas',
help='atlas name',
required=False,
default='aparc.DKTatlas40')
parser.add_argument('-f',
'--function',
help='function name',
required=False,
default='all',
type=au.str_arr_type)
parser.add_argument('--exclude',
help='functions not to run',
required=False,
default='',
type=au.str_arr_type)
parser.add_argument('--mat_fname',
help='matlab connection file name',
required=False,
default='')
parser.add_argument('--mat_field',
help='matlab connection field name',
required=False,
default='')
parser.add_argument('--labels_exclude',
help='rois to exclude',
required=False,
default='unknown,corpuscallosum',
type=au.str_arr_type)
parser.add_argument('--norm_by_percentile',
help='',
required=False,
default=1,
type=au.is_true)
parser.add_argument('--norm_percs',
help='',
required=False,
default='1,99',
type=au.int_arr_type)
parser.add_argument('--stat',
help='',
required=False,
default=STAT_DIFF,
type=int)
parser.add_argument('--windows',
help='',
required=False,
default=0,
type=int)
parser.add_argument('--t_max',
help='',
required=False,
default=0,
type=int)
parser.add_argument('--threshold_percentile',
help='',
required=False,
default=0,
type=int)
parser.add_argument('--threshold',
help='',
required=False,
default=0,
type=float)
parser.add_argument('--color_map', help='', required=False, default='jet')
parser.add_argument('--symetric_colors',
help='',
required=False,
default=1,
type=au.is_true)
parser.add_argument('--data_max',
help='',
required=False,
default=0,
type=float)
parser.add_argument('--data_min',
help='',
required=False,
default=0,
type=float)
parser.add_argument('--n_jobs', help='cpu num', required=False, default=-1)
args = utils.Bag(au.parse_parser(parser, argv))
args.n_jobs = utils.get_n_jobs(args.n_jobs)
if len(args.conditions) == 1:
args.stat = STAT_AVG
print(args)
return args
type=au.is_true)
parser.add_argument('-v',
'--only_verbose',
help='only verbose',
required=False,
default='0',
type=au.is_true)
parser.add_argument('-d',
'--default_folders',
help='default options',
required=False,
default='1',
type=au.is_true)
parser.add_argument('-f',
'--function',
help='functions to run',
required=False,
default='all',
type=au.str_arr_type)
parser.add_argument('--links_file_name',
help='',
required=False,
default='links.csv')
parser.add_argument('--overwrite_links',
help='',
required=False,
default=0,
type=au.is_true)
args = utils.Bag(au.parse_parser(parser))
main(args)
def parse_args(parser, argv):
args = Bag(au.parse_parser(parser, argv))
args.real_atlas = get_full_atlas_name(args.atlas)
if (len(args.subjects) == 0 and args.subject == '') or (len(args.subjects) > 0 and args.subject != ''):
raise Exception('You need to set --subject or --subjects!')
return args
