def build_args_p():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=__doc__)
p.add_argument('operation',
choices=OPERATIONS.keys(),
metavar='OPERATION',
help='The type of operation to be performed on the '
'streamlines. Must\nbe one of the following: '
'%(choices)s.')
p.add_argument('inputs',
metavar='INPUT_FILES',
nargs='+',
help='The list of files that contain the ' +
'streamlines to operate on.')
p.add_argument('output',
metavar='OUTPUT_FILE',
help='The file where the remaining streamlines '
'are saved.')
add_reference(p)
p.add_argument('--precision',
'-p',
metavar='NUMBER_OF_DECIMALS',
type=int,
help='The precision used when comparing streamlines.')
p.add_argument('--no_metadata',
'-n',
action='store_true',
help='Strip the streamline metadata from the output.')
p.add_argument('--save_metadata_indices',
'-m',
action='store_true',
help='Save streamline indices to metadata. Has no '
'effect if --no-data\nis present. Will '
'overwrite \'ids\' metadata if already present.')
p.add_argument('--save_indices',
'-s',
metavar='OUTPUT_INDEX_FILE',
help='Save the streamline indices to the supplied '
'json file.')
add_verbose(p)
add_overwrite_arg(p)
return p
def _buildArgsParser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=DESCRIPTION)
p.add_argument('in_tractogram', help='Path of the input tractogram file.')
p.add_argument('out_tractogram',
help='Path of the output tractogram file.')
add_reference(p)
p.add_argument('--drawn_roi',
nargs=3,
action='append',
metavar=('ROI_NAME', 'MODE', 'CRITERIA'),
help='Filename of a hand drawn ROI (.nii or .nii.gz).')
p.add_argument('--atlas_roi',
nargs=4,
action='append',
metavar=('ROI_NAME', 'ID', 'MODE', 'CRITERIA'),
help='Filename of an atlas (.nii or .nii.gz).')
p.add_argument('--bdo',
dest='bdo',
nargs=3,
action='append',
metavar=('BDO_NAME', 'MODE', 'CRITERIA'),
help='Filename of a bounding box (bdo) file from MI-Brain.')
p.add_argument('--x_plane',
nargs=3,
action='append',
metavar=('PLANE', 'MODE', 'CRITERIA'),
help='Slice number in X, in voxel space.')
p.add_argument('--y_plane',
nargs=3,
action='append',
metavar=('PLANE', 'MODE', 'CRITERIA'),
help='Slice number in Y, in voxel space.')
p.add_argument('--z_plane',
nargs=3,
action='append',
metavar=('PLANE', 'MODE', 'CRITERIA'),
help='Slice number in Z, in voxel space.')
p.add_argument('--filtering_list',
help='Text file containing one rule per line\n'
'(i.e. drawn_roi mask.nii.gz both_ends include).')
p.add_argument('--no_empty',
action='store_true',
help='Do not write file if there is no streamline.')
add_verbose(p)
add_overwrite_arg(p)
return p
def _build_args_parser():
p = argparse.ArgumentParser(
formatter_class=argparse.RawTextHelpFormatter,
description=__doc__,
epilog="""Garyfallidis, E., Côté, M. A., Rheault, F., ... &
Descoteaux, M. (2018). Recognition of white matter
bundles using local and global streamline-based registration and
clustering. NeuroImage, 170, 283-295.""")
p.add_argument('in_tractogram',
help='Input tractogram filename (trk or tck).')
p.add_argument('in_model',
help='Model to use for recognition (trk or tck).')
p.add_argument('transformation',
help='4x4 transformation to bring the model onto \n'
'the input tractogram')
p.add_argument('output_name',
help='Output tractogram filename.')
add_reference(p)
p.add_argument('--wb_clustering_thr', type=float, default=8,
help='Clustering threshold used for the whole brain '
'[%(default)smm].')
p.add_argument('--model_clustering_thr', type=float, default=4,
help='Clustering threshold used for the model '
'[%(default)smm].')
p.add_argument('--pruning_thr', type=float, default=6,
help='MDF threshold used for final streamlines selection '
'[%(default)smm].')
p.add_argument('--slr_threads', type=int, default=None,
help='Number of threads for SLR [all].')
p.add_argument('--seed', type=int, default=None,
help='Random number generator seed [%(default)s].')
p.add_argument('--inverse', action='store_true',
help='Use the inverse transformation.')
p.add_argument('--no_empty', action='store_true',
help='Do not write file if there is no streamline.')
group = p.add_mutually_exclusive_group()
group.add_argument('--input_pickle',
help='Input pickle clusters map file.\n'
'Will override the wb_clustering_thr parameter.')
group.add_argument('--output_pickle',
help='Output pickle clusters map file.')
add_verbose(p)
add_overwrite_arg(p)
return p
def _build_args_parser():
p = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawTextHelpFormatter,
epilog='References: [1] Girard, G., Whittingstall K., Deriche, R., '
'and Descoteaux, M. (2014). Towards quantitative connectivity '
'analysis: reducing tractography biases. Neuroimage, 98, '
'266-278.')
p._optionals.title = 'Generic options'
p.add_argument(
'sh_file',
help='Spherical harmonic file. Data must be aligned with \nseed_file '
'(isotropic resolution, nifti, see --basis).')
p.add_argument('seed_file',
help='Seeding mask (isotropic resolution, nifti).')
p.add_argument(
'map_include_file',
help='The probability map of ending the streamline and \nincluding it '
'in the output (CMC, PFT [1]). \n(isotropic resolution, nifti).')
p.add_argument(
'map_exclude_file',
help='The probability map of ending the streamline and \nexcluding it '
'in the output (CMC, PFT [1]). \n(isotropic resolution, nifti).')
p.add_argument('output_file',
help='Streamline output file (must be trk or tck).')
track_g = p.add_argument_group('Tracking options')
track_g.add_argument(
'--algo',
default='prob',
choices=['det', 'prob'],
help='Algorithm to use (must be "det" or "prob"). [%(default)s]')
track_g.add_argument('--step',
dest='step_size',
type=float,
default=0.5,
help='Step size in mm. [%(default)s]')
track_g.add_argument(
'--min_length',
type=float,
default=10.,
help='Minimum length of a streamline in mm. [%(default)s]')
track_g.add_argument(
'--max_length',
type=float,
default=300.,
help='Maximum length of a streamline in mm. [%(default)s]')
track_g.add_argument(
'--theta',
type=float,
help='Maximum angle between 2 steps. ["det"=45, "prob"=20]')
track_g.add_argument(
'--act',
action='store_true',
help='If set, uses anatomically-constrained tractography (ACT)\n'
'instead of continuous map criterion (CMC).')
track_g.add_argument(
'--sfthres',
dest='sf_threshold',
type=float,
default=0.1,
help='Spherical function relative threshold. [%(default)s]')
track_g.add_argument(
'--sfthres_init',
dest='sf_threshold_init',
type=float,
default=0.5,
help='Spherical function relative threshold value for the \ninitial '
'direction. [%(default)s]')
add_sh_basis_args(track_g)
seed_group = p.add_argument_group(
'Seeding options', 'When no option is provided, uses --npv 1.')
seed_sub_exclusive = seed_group.add_mutually_exclusive_group()
seed_sub_exclusive.add_argument('--npv',
type=int,
help='Number of seeds per voxel.')
seed_sub_exclusive.add_argument('--nt',
type=int,
help='Total number of seeds to use.')
pft_g = p.add_argument_group('PFT options')
pft_g.add_argument(
'--particles',
type=int,
default=15,
help='Number of particles to use for PFT. [%(default)s]')
pft_g.add_argument('--back',
dest='back_tracking',
type=float,
default=2.,
help='Length of PFT back tracking in mm. [%(default)s]')
pft_g.add_argument(
'--forward',
dest='forward_tracking',
type=float,
default=1.,
help='Length of PFT forward tracking in mm. [%(default)s]')
out_g = p.add_argument_group('Output options')
out_g.add_argument(
'--compress',
type=float,
help='If set, will compress streamlines. The parameter\nvalue is the '
'distance threshold. A rule of thumb\nis to set it to 0.1mm for '
'deterministic\nstreamlines and 0.2mm for probabilitic '
'streamlines.')
out_g.add_argument('--all',
dest='keep_all',
action='store_true',
help='If set, keeps "excluded" streamlines.\n'
'NOT RECOMMENDED, except for debugging.')
out_g.add_argument('--seed',
type=int,
help='Random number generator seed.')
add_overwrite_arg(out_g)
log_g = p.add_argument_group('Logging options')
add_verbose(log_g)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
p._optionals.title = 'Generic options'
p.add_argument('sh_file',
help='Spherical harmonic file. \n'
'(isotropic resolution, nifti, see --basis).')
p.add_argument('seed_file',
help='Seeding mask (isotropic resolution, nifti).')
p.add_argument('mask_file',
help='Seeding mask(isotropic resolution, nifti).\n' +
'Tracking will stop outside this mask')
p.add_argument('output_file',
help='Streamline output file (must be trk or tck).')
track_g = p.add_argument_group('Tracking options')
track_g.add_argument(
'--algo',
default='prob',
choices=['det', 'prob'],
help='Algorithm to use (must be "det" or "prob"). [%(default)s]')
track_g.add_argument('--step',
dest='step_size',
type=float,
default=0.5,
help='Step size in mm. [%(default)s]')
track_g.add_argument(
'--min_length',
type=float,
default=10.,
help='Minimum length of a streamline in mm. [%(default)s]')
track_g.add_argument(
'--max_length',
type=float,
default=300.,
help='Maximum length of a streamline in mm. [%(default)s]')
track_g.add_argument(
'--theta',
type=float,
help='Maximum angle between 2 steps. ["eudx"=60, det"=45, "prob"=20]')
track_g.add_argument(
'--sfthres',
dest='sf_threshold',
type=float,
default=0.1,
help='Spherical function relative threshold. [%(default)s]')
add_sh_basis_args(track_g)
seed_group = p.add_argument_group(
'Seeding options', 'When no option is provided, uses --npv 1.')
seed_sub_exclusive = seed_group.add_mutually_exclusive_group()
seed_sub_exclusive.add_argument('--npv',
type=int,
help='Number of seeds per voxel.')
seed_sub_exclusive.add_argument('--nt',
type=int,
help='Total number of seeds to use.')
p.add_argument('--sphere',
choices=sorted(SPHERE_FILES.keys()),
default='symmetric724',
help='Set of directions to be used for tracking')
out_g = p.add_argument_group('Output options')
out_g.add_argument(
'--compress',
type=float,
help='If set, will compress streamlines. The parameter\nvalue is the '
'distance threshold. A rule of thumb\nis to set it to 0.1mm for '
'deterministic\nstreamlines and 0.2mm for probabilitic '
'streamlines.')
out_g.add_argument('--seed',
type=int,
help='Random number generator seed.')
add_overwrite_arg(out_g)
log_g = p.add_argument_group('Logging options')
add_verbose(log_g)
return p