def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('input', metavar='fODFs',
help='Path of the fODF volume in spherical harmonics (SH).')
p.add_argument('fa', metavar='FA',
help='Path to the FA volume.')
p.add_argument('md', metavar='MD',
help='Path to the mean diffusivity (MD) volume.')
p.add_argument(
'--fa_t', dest='fa_threshold', type=float, default='0.1',
help='Maximal threshold of FA (voxels under that threshold are '
'considered for evaluation, default: 0.1)')
p.add_argument(
'--md_t', dest='md_threshold', type=float, default='0.003',
help='Minimal threshold of MD in mm2/s (voxels above that threshold '
'are considered for evaluation, default: 0.003)')
p.add_argument(
'--max_value_output', metavar='file',
help='Output path for the text file containing the value. If not set '
'the file will not be saved.')
p.add_argument(
'--mask_output', metavar='file',
help='Output path for the ventricule mask. If not set, the mask will '
'not be saved.')
add_sh_basis_args(p)
add_overwrite_arg(p)
p.add_argument('-v', action='store_true', dest='verbose',
help='Use verbose output. Default: false.')
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_sh', help='Path to the input file.')
p.add_argument('out_sh', help='File name for averaged signal.')
p.add_argument('--out_sym',
default=None,
help='Name of optional symmetric output. [%(default)s]')
add_sh_basis_args(p)
p.add_argument('--sphere',
default='repulsion724',
choices=sorted(SPHERE_FILES.keys()),
help='Sphere used for the SH to SF projection. '
'[%(default)s]')
p.add_argument('--sharpness',
default=1.0,
type=float,
help='Specify sharpness factor to use for weighted average.'
' [%(default)s]')
p.add_argument('--sigma',
default=1.0,
type=float,
help='Sigma of the gaussian to use. [%(default)s]')
add_verbose_arg(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=__doc__, epilog=EPILOG)
p.add_argument('in_fodfs', metavar='fODFs',
help='Path of the fODF volume in spherical harmonics (SH).')
p.add_argument('in_fa', metavar='FA',
help='Path to the FA volume.')
p.add_argument('in_md', metavar='MD',
help='Path to the mean diffusivity (MD) volume.')
p.add_argument('--fa_t', dest='fa_threshold',
type=float, default='0.1',
help='Maximal threshold of FA (voxels under that threshold'
' are considered for evaluation, [%(default)s]).')
p.add_argument('--md_t', dest='md_threshold',
type=float, default='0.003',
help='Minimal threshold of MD in mm2/s (voxels above that '
'threshold are considered for '
'evaluation, [%(default)s]).')
p.add_argument('--max_value_output', metavar='file',
help='Output path for the text file containing the value. '
'If not set the file will not be saved.')
p.add_argument('--mask_output', metavar='file',
help='Output path for the ventricule mask. If not set, '
'the mask will not be saved.')
add_sh_basis_args(p)
add_verbose_arg(p)
add_overwrite_arg(p)
return p
def add_tracking_options(p):
track_g = p.add_argument_group('Tracking options')
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.,
metavar='m',
help='Minimum length of a streamline in mm. '
'[%(default)s]')
track_g.add_argument('--max_length',
type=float,
default=300.,
metavar='M',
help='Maximum length of a streamline in mm. '
'[%(default)s]')
track_g.add_argument('--theta',
type=float,
help='Maximum angle between 2 steps.\n'
'["eudx"=60, "det"=45, "prob"=20]')
track_g.add_argument('--sfthres',
dest='sf_threshold',
metavar='sf_th',
type=float,
default=0.1,
help='Spherical function relative threshold. '
'[%(default)s]')
add_sh_basis_args(track_g)
return track_g
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_dwi',
help='Path of the dwi volume.')
p.add_argument('in_bval',
help='Path of the b-value file, in FSL format.')
p.add_argument('in_bvec',
help='Path of the b-vector file, in FSL format.')
p.add_argument('out_sh',
help='Name of the output SH file to save.')
p.add_argument('--sh_order', type=int, default=4,
help='SH order to fit (int). [%(default)s]')
add_sh_basis_args(p)
p.add_argument('--smooth', type=float, default=0.006,
help='Lambda-regularization coefficient in the SH fit '
'(float). [%(default)s]')
p.add_argument('--use_attenuation', action='store_true',
help='If set, will use signal attenuation before fitting '
'the SH (i.e. divide by the b0).')
add_force_b0_arg(p)
p.add_argument('--mask',
help='Path to a binary mask.\nOnly data inside the mask '
'will be used for computations and reconstruction ')
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_dwi',
help='Path of the input diffusion volume.')
p.add_argument('in_bval',
help='Path of the bvals file, in FSL format.')
p.add_argument('in_bvec',
help='Path of the bvecs file, in FSL format.')
p.add_argument('frf_file',
help='Path of the FRF file')
p.add_argument('out_fODF',
help='Output path for the fiber ODF coefficients.')
p.add_argument(
'--sh_order', metavar='int', default=8, type=int,
help='SH order used for the CSD. (Default: 8)')
p.add_argument(
'--mask', metavar='',
help='Path to a binary mask. Only the data inside the mask will be '
'used for computations and reconstruction.')
add_force_b0_arg(p)
add_sh_basis_args(p)
add_processes_arg(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
formatter_class=argparse.RawTextHelpFormatter,
description=__doc__,
epilog=EPILOG,
)
p.add_argument('bundle_filename', help='Input bundle filename.')
p.add_argument('fod_filename', help='Input FOD filename.')
p.add_argument('mask_filename',
help='Mask to constrain the TODI spatial smoothing,\n'
'for example a WM mask.')
add_sh_basis_args(p)
p.add_argument('--todi_sigma',
choices=[0, 1, 2, 3, 4],
default=1,
type=int,
help='Smooth the orientation histogram.')
p.add_argument('--sf_threshold',
default=0.2,
type=float,
help='Relative threshold for sf masking (0.0-1.0).')
p.add_argument('--output_prefix',
default='',
help='Add a prefix to all output filename, \n'
'default is no prefix.')
p.add_argument('--output_dir',
default='./',
help='Output directory for all generated files,\n'
'default is current directory.')
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
epilog=EPILOG,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_sh', help='Input SH image.')
p.add_argument('--mask', default='', help='Optional mask.')
# outputs
p.add_argument('--cos_asym_map',
default='',
help='Output asymmetry map using cos similarity.')
p.add_argument('--odd_power_map', default='', help='Output odd power map.')
p.add_argument('--peaks',
default='',
help='Output filename for the extracted peaks.')
p.add_argument('--peak_values',
default='',
help='Output filename for the extracted peaks values.')
p.add_argument('--peak_indices',
default='',
help='Output filename for the generated peaks indices on '
'the sphere.')
p.add_argument('--nupeaks',
default='',
help='Output filename for the nupeaks file.')
p.add_argument('--not_all',
action='store_true',
help='If set, only saves the files specified using the '
'file flags [%(default)s].')
p.add_argument('--at',
dest='a_threshold',
type=float,
default='0.0',
help='Absolute threshold on fODF amplitude. This '
'value should be set to\napproximately 1.5 to 2 times '
'the maximum fODF amplitude in isotropic voxels\n'
'(ie. ventricles).\n'
'Use compute_fodf_max_in_ventricles.py to find the '
'maximal value.\n'
'See [Dell\'Acqua et al HBM 2013] [%(default)s].')
p.add_argument('--rt',
dest='r_threshold',
type=float,
default='0.1',
help='Relative threshold on fODF amplitude in percentage '
'[%(default)s].')
p.add_argument('--sphere',
default='symmetric724',
choices=sorted(SPHERE_FILES.keys()),
help='Sphere to use for peak directions estimation '
'[%(default)s].')
add_processes_arg(p)
add_sh_basis_args(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
p.add_argument('in_dwi', help='Path of the input diffusion volume.')
p.add_argument('in_bval', help='Path of the bval file, in FSL format.')
p.add_argument('in_bvec', help='Path of the bvec file, in FSL format.')
p.add_argument('in_wm_frf', help='Text file of WM response function.')
p.add_argument('in_gm_frf', help='Text file of GM response function.')
p.add_argument('in_csf_frf', help='Text file of CSF response function.')
p.add_argument('--sh_order',
metavar='int',
default=8,
type=int,
help='SH order used for the CSD. (Default: 8)')
p.add_argument('--mask',
metavar='',
help='Path to a binary mask. Only the data inside the '
'mask will be used for computations and reconstruction.')
add_force_b0_arg(p)
add_sh_basis_args(p)
add_processes_arg(p)
add_overwrite_arg(p)
p.add_argument('--not_all',
action='store_true',
help='If set, only saves the files specified using the '
'file flags. (Default: False)')
g = p.add_argument_group(title='File flags')
g.add_argument('--wm_out_fODF',
metavar='file',
default='',
help='Output filename for the WM fODF coefficients.')
g.add_argument('--gm_out_fODF',
metavar='file',
default='',
help='Output filename for the GM fODF coefficients.')
g.add_argument('--csf_out_fODF',
metavar='file',
default='',
help='Output filename for the CSF fODF coefficients.')
g.add_argument('--vf',
metavar='file',
default='',
help='Output filename for the volume fractions map.')
g.add_argument('--vf_rgb',
metavar='file',
default='',
help='Output filename for the volume fractions map in rgb.')
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_dwi', help='Path of the input diffusion volume.')
p.add_argument('in_bval', help='Path of the bvals file, in FSL format.')
p.add_argument('in_bvec', help='Path of the bvecs file, in FSL format.')
add_overwrite_arg(p)
p.add_argument('--sh_order',
default=4,
type=int,
help='Spherical harmonics order. Must be a positive even '
'number [%(default)s].')
p.add_argument('--mask',
help='Path to a binary mask. Only data inside the mask will'
' be used for computations and reconstruction '
'[%(default)s].')
p.add_argument('--use_qball',
action='store_true',
help='If set, qball will be used as the odf reconstruction'
' model instead of CSA.')
p.add_argument('--not_all',
action='store_true',
help='If set, will only save the files specified using the '
'following flags.')
g = p.add_argument_group(title='File flags')
g.add_argument('--gfa',
default='',
help='Output filename for the generalized fractional '
'anisotropy [gfa.nii.gz].')
g.add_argument('--peaks',
default='',
help='Output filename for the extracted peaks '
'[peaks.nii.gz].')
g.add_argument('--peak_indices',
default='',
help='Output filename for the generated peaks '
'indices on the sphere [peaks_indices.nii.gz].')
g.add_argument('--sh',
default='',
help='Output filename for the spherical harmonics '
'coefficients [sh.nii.gz].')
g.add_argument('--nufo',
default='',
help='Output filename for the NUFO map [nufo.nii.gz].')
g.add_argument('--a_power',
default='',
help='Output filename for the anisotropic power map'
'[anisotropic_power.nii.gz].')
add_force_b0_arg(p)
add_sh_basis_args(p)
add_processes_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
p.add_argument(
'input', metavar='fODFs',
help='Path of the fODF volume in spherical harmonics (SH).')
p.add_argument(
'at', metavar='a_threshold', type=float,
help='WARNING!!! EXTREMELY IMPORTANT PARAMETER, VARIABLE '
'ACROSS DATASETS!!!\nAbsolute threshold on fODF amplitude.\nThis '
'value should set to approximately 1.5 to 2 times the maximum\n'
'fODF amplitude in isotropic voxels (ex. ventricles).\n'
'compute_fodf_max_in_ventricles.py can be used to find the '
'maximal value.\nSee [Dell\'Acqua et al HBM 2013].')
p.add_argument(
'--sphere', metavar='string', default='repulsion724',
choices=['repulsion100', 'repulsion724'],
help='Discrete sphere to use in the processing. [%(default)s].')
p.add_argument(
'--mask', metavar='',
help='Path to a binary mask. Only the data inside the mask will be '
'used for computations and reconstruction [%(default)s].')
p.add_argument(
'--rt', dest='r_threshold', type=float, default='0.1',
help='Relative threshold on fODF amplitude in percentage '
'[%(default)s].')
add_sh_basis_args(p)
add_overwrite_arg(p)
p.add_argument(
'--vis', dest='visu', action='store_true',
help='Export map for better visualization in FiberNavigator.\n'
'!WARNING! these maps should not be used to compute statistics '
'[%(default)s].')
p.add_argument(
'--not_all', action='store_true',
help='If set, only saves the files specified using the file flags '
'[%(default)s].')
g = p.add_argument_group(title='File flags')
g.add_argument(
'--afd', metavar='file', default='',
help='Output filename for the AFD_max map.')
g.add_argument(
'--afd_total', metavar='file', default='',
help='Output filename for the AFD_total map (SH coeff = 0).')
g.add_argument(
'--afd_sum', metavar='file', default='',
help='Output filename for the sum of all peak contributions (sum of '
'fODF lobes on the sphere).')
g.add_argument('--nufo', metavar='file', default='',
help='Output filename for the NuFO map.')
g.add_argument('--peaks', metavar='file', default='',
help='Output filename for the extracted peaks.')
return p
def _build_arg_parser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=__doc__)
p.add_argument('input_sh', help='Input SH filename. (nii or nii.gz)')
p.add_argument('output_name', help='Name of the output file.')
add_sh_basis_args(p, mandatory=True)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('input', help='Path of the input diffusion volume.')
p.add_argument('bvals', help='Path of the bvals file, in FSL format.')
p.add_argument('bvecs', help='Path of the bvecs file, in FSL format.')
p.add_argument('frf_file', help='Path of the FRF file')
p.add_argument('--sh_order',
metavar='int',
default=8,
type=int,
help='SH order used for the CSD. (Default: 8)')
p.add_argument(
'--mask',
metavar='',
help='Path to a binary mask. Only the data inside the mask will be '
'used for computations and reconstruction.')
p.add_argument(
'--processes',
dest='nbr_processes',
metavar='NBR',
type=int,
help='Number of sub processes to start. Default : cpu count')
p.add_argument(
'--not_all',
action='store_true',
help='If set, only saves the files specified using the file flags. '
'(Default: False)')
add_force_b0_arg(p)
add_sh_basis_args(p)
g = p.add_argument_group(title='File flags')
g.add_argument('--fodf',
metavar='file',
default='',
help='Output filename for the fiber ODF coefficients.')
g.add_argument('--peaks',
metavar='file',
default='',
help='Output filename for the extracted peaks.')
g.add_argument(
'--peak_indices',
metavar='file',
default='',
help='Output filename for the generated peaks indices on the sphere.')
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
epilog=EPILOG,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_tractogram', help='Input streamlines file.')
add_reference_arg(p)
p.add_argument('--sphere',
default='repulsion724',
help='sphere used for the angular discretization. '
'[%(default)s]')
p.add_argument('--mask', help='Use the given mask.')
p.add_argument('--out_mask', help='Mask showing where TDI > 0.')
p.add_argument('--out_tdi', help='Output Track Density Image (TDI).')
p.add_argument('--out_todi_sf',
help='Output TODI, with SF (each directions\n'
'on the sphere, requires a lot of memory)')
p.add_argument('--out_todi_sh', help='Output TODI, with SH coefficients.')
p.add_argument('--sh_order',
type=int,
default=8,
help='Order of the original SH. [%(default)s]')
p.add_argument('--normalize_per_voxel',
action='store_true',
help='Normalize each SF/SH at each voxel [%(default)s].')
p.add_argument('--smooth_todi',
action='store_true',
help='Smooth TODI (angular and spatial) [%(default)s].')
p.add_argument('--asymmetric',
action='store_true',
help='Compute asymmetric TODI [%(default)s].')
p.add_argument('--n_steps',
default=1,
type=int,
help='Number of steps for streamline segments '
'subdivision prior to binning [%(default)s].')
add_sh_basis_args(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_fODF',
help='Path of the fODF volume in spherical harmonics (SH).')
p.add_argument('--sphere', metavar='string', default='repulsion724',
choices=['repulsion100', 'repulsion724'],
help='Discrete sphere to use in the processing '
'[%(default)s].')
p.add_argument('--mask', metavar='',
help='Path to a binary mask. Only the data inside the mask\n'
'will beused for computations and reconstruction '
'[%(default)s].')
p.add_argument('--at', dest='a_threshold', type=float, default='0.0',
help='Absolute threshold on fODF amplitude. This '
'value should be set to\napproximately 1.5 to 2 times '
'the maximum fODF amplitude in isotropic voxels\n'
'(ie. ventricles).\nUse compute_fodf_max_in_ventricles.py '
'to find the maximal value.\n'
'See [Dell\'Acqua et al HBM 2013] [%(default)s].')
p.add_argument('--rt', dest='r_threshold', type=float, default='0.1',
help='Relative threshold on fODF amplitude in percentage '
'[%(default)s].')
add_sh_basis_args(p)
add_overwrite_arg(p)
add_processes_arg(p)
p.add_argument('--not_all', action='store_true',
help='If set, only saves the files specified using the '
'file flags [%(default)s].')
g = p.add_argument_group(title='File flags')
g.add_argument('--afd_max', metavar='file', default='',
help='Output filename for the AFD_max map.')
g.add_argument('--afd_total', metavar='file', default='',
help='Output filename for the AFD_total map (SH coeff = 0).')
g.add_argument('--afd_sum', metavar='file', default='',
help='Output filename for the sum of all peak contributions\n'
'(sum of fODF lobes on the sphere).')
g.add_argument('--nufo', metavar='file', default='',
help='Output filename for the NuFO map.')
g.add_argument('--rgb', metavar='file', default='',
help='Output filename for the RGB map.')
g.add_argument('--peaks', metavar='file', default='',
help='Output filename for the extracted peaks.')
g.add_argument('--peak_values', metavar='file', default='',
help='Output filename for the extracted peaks values.')
g.add_argument('--peak_indices', metavar='file', default='',
help='Output filename for the generated peaks indices on '
'the sphere.')
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_sh', help='Path of the SH volume.')
p.add_argument('out_sf',
help='Name of the output SF file to save (bvals/bvecs will '
'be automatically named when necessary).')
# Sphere vs bvecs choice for SF
directions = p.add_mutually_exclusive_group(required=True)
directions.add_argument('--sphere',
choices=sorted(SPHERE_FILES.keys()),
help='Sphere used for the SH to SF projection. ')
directions.add_argument(
'--in_bvec', help="Directions used for the SH to SF projection.")
p.add_argument('--dtype',
default="float32",
choices=["float32", "float64"],
help="Datatype to use for SF computation and output array."
"'[%(default)s]'")
# Optional args for a DWI-like volume
p.add_argument('--in_bval',
help='b-value file, in FSL format, '
'used to assign a b-value to the '
'output SF and generate a `.bval` file.')
p.add_argument('--in_b0',
help='b0 volume to concatenate to the '
'final SF volume.')
p.add_argument('--out_bval', help="Optional output bval file.")
p.add_argument('--out_bvec', help="Optional output bvec file.")
p.add_argument('--b0_scaling',
action="store_true",
help="Scale resulting SF by the b0 image.")
add_sh_basis_args(p)
p.add_argument('--full_basis',
action="store_true",
help="If true, use a full basis for the input SH "
"coefficients.")
add_processes_arg(p)
add_overwrite_arg(p)
add_force_b0_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_sh', help='Path to the input file.')
p.add_argument('out_sh', help='File name for averaged signal.')
p.add_argument('--out_asymmetry',
default='asym_map.nii.gz',
help='File name for asymmetry map. Can only be outputed'
' when the output SH basis is full. [%(default)s]')
p.add_argument('--sh_order',
default=8,
type=int,
help='SH order of the input. [%(default)s]')
add_sh_basis_args(p)
p.add_argument('--sphere',
default='repulsion724',
choices=sorted(SPHERE_FILES.keys()),
help='Sphere used for the SH to SF projection. '
'[%(default)s]')
p.add_argument('--sharpness',
default=1.0,
type=float,
help='Specify sharpness factor to use for weighted average.'
' [%(default)s]')
p.add_argument('--sigma',
default=1.0,
type=float,
help='Sigma of the gaussian to use. [%(default)s]')
p.add_argument('--out_sym',
action='store_true',
help='If set, saves output in symmetric SH basis.')
add_verbose_arg(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
epilog=EPILOG,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_bundle', help='Path of the bundle file.')
p.add_argument('in_fodf',
help='Path of the fODF volume in spherical harmonics (SH).')
p.add_argument('afd_mean_map', help='Path of the output mean AFD map.')
p.add_argument('--length_weighting',
action='store_true',
help='If set, will weigh the AFD values according to '
'segment lengths. [%(default)s]')
add_reference_arg(p)
add_sh_basis_args(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_hdf5',
help='HDF5 filename (.h5) containing decomposed '
'connections.')
p.add_argument('in_fodf',
help='Path of the fODF volume in spherical harmonics (SH).')
p.add_argument('out_hdf5',
help='Path of the output HDF5 filenames (.h5).')
p.add_argument('--length_weighting', action='store_true',
help='If set, will weigh the AFD values according to '
'segment lengths. [%(default)s]')
add_processes_arg(p)
add_sh_basis_args(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawTextHelpFormatter)
# TODO Rename argument in_bundle
p.add_argument('tract_filename',
help='Input streamlines file.')
add_reference_arg(p)
# TODO Uniformize argparse
p.add_argument('--sphere', default='repulsion724',
help='sphere used for the angular discretization.')
p.add_argument('--mask',
help='Use the given mask')
p.add_argument('--out_mask',
help='Mask showing where TDI > 0.')
p.add_argument('--out_lw_tdi',
help='Output length-weighted TDI map.')
p.add_argument('--out_lw_todi',
help='Output length-weighted TODI map.')
p.add_argument('--out_lw_todi_sh',
help='Output length-weighted TODI map, '
'with SH coefficient.')
p.add_argument('--sh_order', type=int, default=8,
help='Order of the original SH.')
p.add_argument('--sh_normed', action='store_true',
help='Normalize sh.')
p.add_argument('--smooth', action='store_true',
help='Smooth todi (angular and spatial).')
add_sh_basis_args(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_sh',
help='Path to the input file.')
p.add_argument('out_sh',
help='File name for averaged signal.')
add_sh_basis_args(p)
p.add_argument('--out_sym', default=None,
help='Name of optional symmetric output. [%(default)s]')
p.add_argument('--sphere', default='repulsion724',
choices=sorted(SPHERE_FILES.keys()),
help='Sphere used for the SH to SF projection. '
'[%(default)s]')
p.add_argument('--sigma_angular', default=1.0, type=float,
help='Standard deviation for angular distance.'
' [%(default)s]')
p.add_argument('--sigma_spatial', default=1.0, type=float,
help='Standard deviation for spatial distance.'
' [%(default)s]')
p.add_argument('--sigma_range', default=1.0, type=float,
help='Standard deviation for range filter.'
' [%(default)s]')
p.add_argument('--use_gpu', action='store_true',
help='Use GPU for computation.')
add_verbose_arg(p)
add_overwrite_arg(p)
add_processes_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__,
epilog=EPILOG,
formatter_class=argparse.RawTextHelpFormatter)
# rename `optional arguments` group to `Generic options`
p._optionals.title = 'Generic options'
# mandatory tracking options
add_mandatory_options_tracking(p)
track_g = p.add_argument_group('Tracking options')
track_g.add_argument('--step_size',
type=float,
default=0.5,
help='Step size in mm. [%(default)s]')
track_g.add_argument('--theta',
type=float,
nargs='+',
default=20.0,
help='Maximum angle between 2 steps. If more than one'
' value\nare given, the maximum angle will be '
'drawn at random\nfrom the distribution for each'
' streamline. [%(default)s]')
track_g.add_argument('--min_length',
type=float,
default=20.0,
help='Minimum length of the streamline '
'in mm. [%(default)s]')
track_g.add_argument('--max_length',
type=float,
default=300.0,
help='Maximum length of the streamline '
'in mm. [%(default)s]')
track_g.add_argument('--forward_only',
action='store_true',
help='Only perform forward tracking.')
add_sh_basis_args(track_g)
# seeding options
add_seeding_options(p)
out_g = p.add_argument_group('Output options')
out_g.add_argument('--save_seeds',
action='store_true',
help='Save seed positions in data_per_streamline.')
out_g.add_argument('--compress',
type=float,
help='Compress streamlines using the given threshold.')
# random number generator for SF sampling
out_g.add_argument('--rng_seed',
type=int,
help='Random number generator seed.')
add_overwrite_arg(out_g)
gpu_g = p.add_argument_group('GPU options')
gpu_g.add_argument('--batch_size',
type=int,
default=100000,
help='Approximate size of GPU batches (number\n'
'of streamlines to track in parallel).'
' [%(default)s]')
log_g = p.add_argument_group('Logging options')
add_verbose_arg(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
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
# Positional arguments
p.add_argument('in_fodf', default=None, help='Input SH image file.')
# Window configuration options
p.add_argument('--slice_index',
type=int,
help='Index of the slice to visualize along a given axis. '
'Defaults to middle of volume.')
p.add_argument('--win_dims',
nargs=2,
metavar=('WIDTH', 'HEIGHT'),
default=(768, 768),
type=int,
help='The dimensions for the vtk window. [%(default)s]')
p.add_argument('--interactor',
default='trackball',
choices={'image', 'trackball'},
help='Specify interactor mode for vtk window. '
'[%(default)s]')
p.add_argument('--axis_name',
default='axial',
type=str,
choices={'axial', 'coronal', 'sagittal'},
help='Name of the axis to visualize. [%(default)s]')
p.add_argument('--silent',
action='store_true',
help='Disable interactive visualization.')
p.add_argument('--output', help='Path to output file.')
add_overwrite_arg(p)
# Optional FODF personalization arguments
add_sh_basis_args(p)
sphere_choices = {
'symmetric362', 'symmetric642', 'symmetric724', 'repulsion724',
'repulsion100', 'repulsion200'
}
p.add_argument('--sphere',
default='symmetric724',
choices=sphere_choices,
help='Name of the sphere used to reconstruct SF. '
'[%(default)s]')
p.add_argument('--sph_subdivide',
type=int,
help='Number of subdivisions for given sphere. If not '
'supplied, use the given sphere as is.')
p.add_argument('--mask',
help='Optional mask file. Only fODF inside '
'the mask are displayed.')
p.add_argument('--colormap',
default=None,
help='Colormap for the ODF slicer. If None, '
'then a RGB colormap will be used. [%(default)s]')
p.add_argument('--scale',
default=0.5,
type=float,
help='Scaling factor for FODF. [%(default)s]')
p.add_argument('--radial_scale_off',
action='store_true',
help='Disable radial scale for ODF slicer.')
p.add_argument('--norm_off',
action='store_true',
help='Disable normalization of ODF slicer.')
# Background image options
p.add_argument('--background',
help='Background image file. If RGB, values must '
'be between 0 and 255.')
p.add_argument('--bg_range',
nargs=2,
metavar=('MIN', 'MAX'),
type=float,
help='The range of values mapped to range [0, 1] '
'for background image. [(bg.min(), bg.max())]')
p.add_argument('--bg_opacity',
type=float,
default=1.0,
help='The opacity of the background image. Opacity of 0.0 '
'means transparent and 1.0 is completely visible. '
'[%(default)s]')
p.add_argument('--bg_offset',
type=float,
default=0.5,
help='The offset of the background image. [%(default)s]')
p.add_argument('--bg_interpolation',
default='nearest',
choices={'linear', 'nearest'},
help='Interpolation mode for the background image. '
'[%(default)s]')
# Peaks input file options
p.add_argument('--peaks', help='Peaks image file.')
p.add_argument('--peaks_color',
nargs=3,
type=float,
help='Color used for peaks. If None, '
'then a RGB colormap is used. [%(default)s]')
p.add_argument('--peaks_width',
default=1.0,
type=float,
help='Width of peaks segments. [%(default)s]')
peaks_scale_group = p.add_mutually_exclusive_group()
peaks_scale_group.add_argument('--peaks_values', help='Peaks values file.')
peaks_scale_group.add_argument('--peaks_length',
default=0.65,
type=float,
help='Length of the peaks segments. '
'[%(default)s]')
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p._optionals.title = 'Generic options'
p.add_argument('in_sh',
help='Spherical harmonic file (.nii.gz) OR \n'
'peaks/evecs (.nii.gz) for EUDX tracking.')
p.add_argument('in_seed', help='Seeding mask (.nii.gz).')
p.add_argument('in_mask',
help='Seeding mask (.nii.gz).\n'
'Tracking will stop outside this mask.')
p.add_argument('out_tractogram',
help='Tractogram 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', 'eudx'],
help='Algorithm to use [%(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.\n'
'["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.\n'
'The parameter value is the distance threshold.')
out_g.add_argument('--seed',
type=int,
help='Random number generator seed.')
add_overwrite_arg(out_g)
out_g.add_argument('--save_seeds',
action='store_true',
help='If set, save the seeds used for the tracking \n '
'in the data_per_streamline property.')
log_g = p.add_argument_group('Logging options')
add_verbose_arg(log_g)
return p
