def _build_args_parser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description='Filter streamlines by length.')
p.add_argument('in_tractogram', help='Streamlines input file name.')
p.add_argument('out_tractogram', help='Streamlines output file name.')
p.add_argument('--minL',
default=0.,
type=float,
help='Minimum length of streamlines. [%(default)s]')
p.add_argument('--maxL',
default=np.inf,
type=float,
help='Maximum length of streamlines. [%(default)s]')
p.add_argument('--no_empty',
action='store_true',
help='Do not write file if there is no streamline.')
p.add_argument('--display_counts',
action='store_true',
help='Print streamline count before and after filtering')
add_reference_arg(p)
add_overwrite_arg(p)
add_verbose_arg(p)
add_json_args(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_bundles', nargs='+',
help='Path of the input bundles.')
p.add_argument('out_json',
help='Path of the output json file.')
p.add_argument('--streamline_dice', action='store_true',
help='Streamlines-wise Dice coefficient will be computed \n'
'Tractograms must be identical [%(default)s].')
p.add_argument('--disable_streamline_distance', action='store_true',
help='Will not compute the streamlines distance \n'
'[%(default)s].')
p.add_argument('--single_compare',
help='Compare inputs to this single file.')
p.add_argument('--keep_tmp', action='store_true',
help='Will not delete the tmp folder at the end.')
add_processes_arg(p)
add_reference_arg(p)
add_json_args(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=__doc__)
p.add_argument('in_tractogram',
help='Tractogram input file name.')
p.add_argument('out_tractogram',
help='Output tractogram without loops.')
p.add_argument('--looping_tractogram',
help='If set, saves detected looping streamlines.')
p.add_argument('--qb', action='store_true',
help='If set, uses QuickBundles to detect\n' +
'outliers (loops, sharp angle turns).\n' +
'Should mainly be used with bundles. '
'[%(default)s]')
p.add_argument('--threshold', default=8., type=float,
help='Maximal streamline to bundle distance\n' +
'for a streamline to be considered as\n' +
'a tracking error. [%(default)s]')
p.add_argument('-a', dest='angle', default=360, type=float,
help='Maximum looping (or turning) angle of\n' +
'a streamline in degrees. [%(default)s]')
p.add_argument('--display_counts', action='store_true',
help='Print streamline count before and after filtering')
add_overwrite_arg(p)
add_reference_arg(p)
add_json_args(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_lesion',
help='Binary mask of the lesion(s) (.nii.gz).')
p.add_argument('out_json',
help='Output file for lesion information (.json).')
p1 = p.add_mutually_exclusive_group()
p1.add_argument('--bundle',
help='Path of the bundle file (.trk).')
p1.add_argument('--bundle_mask',
help='Path of the bundle binary mask (.nii.gz).')
p1.add_argument('--bundle_labels_map',
help='Path of the bundle labels map (.nii.gz).')
p.add_argument('--min_lesion_vol', type=float, default=7,
help='Minimum lesion volume in mm3 [%(default)s].')
p.add_argument('--out_lesion_atlas', metavar='FILE',
help='Save the labelized lesion(s) map (.nii.gz).')
p.add_argument('--out_lesion_stats', metavar='FILE',
help='Save the lesion-wise volume measure (.json).')
p.add_argument('--out_streamlines_stats', metavar='FILE',
help='Save the lesion-wise streamline count (.json).')
add_json_args(p)
add_overwrite_arg(p)
add_reference_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_bundles', nargs='+',
help='Path of the input bundles.')
p.add_argument('out_json',
help='Path of the output json file.')
p.add_argument('--streamline_dice', action='store_true',
help='Compute streamline-wise dice coefficient.\n'
'Tractograms must be identical [%(default)s].')
p.add_argument('--bundle_adjency_no_overlap', action='store_true',
help='If set, do not count zeros in the average BA.')
p.add_argument('--disable_streamline_distance', action='store_true',
help='Will not compute the streamlines distance \n'
'[%(default)s].')
p.add_argument('--single_compare',
help='Compare inputs to this single file.')
p.add_argument('--keep_tmp', action='store_true',
help='Will not delete the tmp folder at the end.')
p.add_argument('--ratio', action='store_true',
help='Compute overlap and overreach as a ratio over the\n'
'reference tractogram in a Tractometer-style way.\n'
'Can only be used if also using the `single_compare` '
'option.')
add_processes_arg(p)
add_reference_arg(p)
add_json_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_bundle',
help='Fiber bundle file to compute statistics on.')
p.add_argument('in_label_map',
help='Label map (.npz) of the corresponding fiber bundle.')
p.add_argument('in_distance_map',
help='Distance map (.npz) of the corresponding bundle/'
'centroid streamline.')
p.add_argument('in_metrics', nargs='+',
help='Nifti file to compute statistics on. Probably some '
'tractometry measure(s) such as FA, MD, RD, ...')
p.add_argument('--density_weighting', action='store_true',
help='If set, weight statistics by the number of '
'streamlines passing through each voxel.')
p.add_argument('--distance_weighting', action='store_true',
help='If set, weight statistics by the inverse of the '
'distance between a streamline and the centroid.')
p.add_argument('--out_json',
help='Path of the output json file. If not given, json '
'formatted stats are simply printed.')
add_overwrite_arg(p)
add_reference_arg(p)
add_json_args(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=__doc__)
p.add_argument('in_bundle',
help='Fiber bundle file to compute the bundle profiles on.')
p.add_argument('in_metrics',
nargs='+',
help='Metric(s) on which to compute the bundle profiles.')
g = p.add_mutually_exclusive_group()
g.add_argument('--in_centroid',
help='If provided it will be used to make sure all '
'streamlines go in the same direction. \n'
'Also, number of points per streamline will be '
'set according to centroid.')
g.add_argument('--nb_pts_per_streamline',
type=int,
default=20,
help='If centroid not provided, resample each streamline to'
' this number of points [%(default)s].')
add_json_args(p)
add_reference_arg(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
p.add_argument('in_bundle',
help='Fiber bundle file to compute statistics on.')
p.add_argument('label_map',
help='Label map (.npz) of the corresponding '
'fiber bundle.')
p.add_argument('distance_map',
help='Distance map (.npz) of the corresponding '
'bundle/centroid streamline.')
p.add_argument('metrics',
nargs='+',
help='Nifti metric(s) to compute statistics on.')
p.add_argument('--density_weighting',
action='store_true',
help='If set, weight statistics by the number of '
'streamlines passing through each voxel.')
p.add_argument('--distance_weighting',
action='store_true',
help='If set, weight statistics by the inverse of the '
'distance between a streamline and the centroid.')
add_reference_arg(p)
add_json_args(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=__doc__)
p.add_argument('in_json',
nargs='+',
help='List of json files to merge (.json).')
p.add_argument('out_json', help='Output json file (.json).')
p.add_argument('--keep_separate',
action='store_true',
help='Merge entries as separate keys based on filename.')
p.add_argument('--no_list',
action='store_true',
help='Merge entries knowing there is no conflict.')
p.add_argument('--add_parent_key',
help='Merge all entries under a single parent.')
p.add_argument('--remove_parent_key',
action='store_true',
help='Merge ignoring parent key (e.g for population).')
p.add_argument('--recursive',
action='store_true',
help='Merge all entries at the lowest layers.')
p.add_argument('--average_last_layer',
action='store_true',
help='Average all entries at the lowest layers.')
add_json_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_mask',
help='Mask volume filename.\nCan be a binary mask or a '
'weighted mask.')
p_metric = p.add_argument_group('Metrics input options')
g_metric = p_metric.add_mutually_exclusive_group(required=True)
g_metric.add_argument('--metrics_dir',
help='Metrics files directory. Name of the '
'directory containing the metrics files.')
g_metric.add_argument('--metrics',
dest='metrics_file_list',
nargs='+',
help='Metrics nifti filename. List of the names of '
'the metrics file, in nifti format.')
p.add_argument('--bin',
action='store_true',
help='If set, will consider every value of the mask '
'higher than 0 to be part of the mask, and set to 1 '
'(equivalent weighting for every voxel).')
p.add_argument('--normalize_weights',
action='store_true',
help='If set, the weights will be normalized to the [0,1] '
'range.')
add_overwrite_arg(p)
add_json_args(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument(
'in_masks',
nargs='+',
help='Masks volume filename (ROI).\nCan be a binary mask or a '
'weighted mask.')
p.add_argument('--metrics',
nargs='+',
required=True,
help='Metrics nifti filename. List of the names of '
'the metrics file, in nifti format.')
p.add_argument('--masks_sum',
action='store_true',
help='Compute the sum of all values in masks '
'(similar to vox count)')
p.add_argument('--save_avg',
help='Save all average to a file (txt, npy, json)\n'
'Otherwise it print the average in ')
add_overwrite_arg(p)
add_json_args(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=__doc__)
p.add_argument('in_tractogram', help='Tractogram input file name.')
p.add_argument('out_tractogram', help='Output tractogram file name.')
p.add_argument('--minU',
default=0.5,
type=float,
help='Min ufactor value. [%(default)s]')
p.add_argument('--maxU',
default=1.0,
type=float,
help='Max ufactor value. [%(default)s]')
p.add_argument('--remaining_tractogram',
help='If set, saves remaining streamlines.')
p.add_argument('--no_empty',
action='store_true',
help='Do not write file if there is no streamline.')
p.add_argument('--display_counts',
action='store_true',
help='Print streamline count before and after filtering.')
add_overwrite_arg(p)
add_reference_arg(p)
add_json_args(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter,
epilog=EPILOG)
p.add_argument('in_conn_matrix',
help='Input connectivity matrix (.npy).\n'
'Typically a streamline count weighted matrix.')
p.add_argument('in_length_matrix',
help='Input length weighted matrix (.npy).')
p.add_argument('out_json', help='Path of the output json.')
p.add_argument('--filtering_mask',
help='Binary filtering mask to apply before computing the '
'measures.')
p.add_argument('--avg_node_wise',
action='store_true',
help='Return a single value for node-wise measures.')
p.add_argument('--append_json',
action='store_true',
help='If the file already exists, will append to the '
'dictionary.')
p.add_argument('--small_world',
action='store_true',
help='Compute measure related to small worldness (omega '
'and sigma).\n This option is much slower.')
add_json_args(p)
add_verbose_arg(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=__doc__)
p.add_argument('in_tractogram', help='Streamlines input file name.')
p.add_argument('out_tractogram', help='Streamlines output file name.')
p.add_argument('--min_x',
default=0.,
type=float,
help='Minimum distance in the first dimension, in mm.'
'[%(default)s]')
p.add_argument('--max_x',
default=np.inf,
type=float,
help='Maximum distance in the first dimension, in mm.'
'[%(default)s]')
p.add_argument('--min_y',
default=0.,
type=float,
help='Minimum distance in the second dimension, in mm.'
'[%(default)s]')
p.add_argument('--max_y',
default=np.inf,
type=float,
help='Maximum distance in the second dimension, in mm.'
'[%(default)s]')
p.add_argument('--min_z',
default=0.,
type=float,
help='Minimum distance in the third dimension, in mm.'
'[%(default)s]')
p.add_argument('--max_z',
default=np.inf,
type=float,
help='Maximum distance in the third dimension, in mm.'
'[%(default)s]')
p.add_argument('--use_abs',
action='store_true',
help="If set, will use the total of distances in absolute "
"value (ex, coming back on yourself will contribute "
"to the total distance instead of cancelling it).")
p.add_argument('--no_empty',
action='store_true',
help='Do not write file if there is no streamline.')
p.add_argument('--display_counts',
action='store_true',
help='Print streamline count before and after filtering.')
p.add_argument('--save_rejected',
metavar='filename',
help="Save the SFT of rejected streamlines.")
add_reference_arg(p)
add_overwrite_arg(p)
add_verbose_arg(p)
add_json_args(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_tractogram',
help='Path of the input tractogram file.')
add_json_args(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument("in_tractogram", help="Input tractogram to score")
p.add_argument("gt_config",
help=".json dict configured as specified above.")
p.add_argument("out_dir", help="Output directory.")
g = p.add_argument_group("Additions to gt_config")
p.add_argument("--gt_dir",
metavar='DIR',
help="Root path of the ground truth files listed in the "
"gt_config.\n If not set, filenames in the config "
"file are considered\n as complete paths.")
g.add_argument("--use_gt_masks_as_limits_masks",
action='store_true',
help="If set, the gt_config's 'gt_mask' will also be used "
"as\n'limits_mask' for each bundle. Note that this "
"means the\nOR will necessarily be 0.")
g = p.add_argument_group("Preprocessing")
g.add_argument("--dilate_endpoints",
metavar="NB_PASS",
default=0,
type=int,
help="Dilate inclusion masks n-times. Default: 0.")
g.add_argument("--remove_invalid",
action="store_true",
help="Remove invalid streamlines before scoring.")
g = p.add_argument_group("Tractometry choices")
g.add_argument("--save_wpc_separately",
action='store_true',
help="If set, streamlines rejected from VC based on the "
"config\nfile criteria will be saved separately from "
"IS (and IC)\nin one file *_WPC.tck per bundle.")
g.add_argument("--compute_ic",
action='store_true',
help="If set, IS are split into NC + IC, where IC are "
"computed as one bundle per\npair of ROI not "
"belonging to a true connection, named\n*_*_IC.tck.")
g.add_argument("--remove_wpc_belonging_to_another_bundle",
action='store_true',
help="If set, WPC actually belonging to VC (from another "
"bundle,\nof course; in the case of overlapping ROIs) "
"will be removed\nfrom the WPC classification.")
p.add_argument("--no_empty",
action='store_true',
help='Do not write file if there is no streamline.')
add_json_args(p)
add_overwrite_arg(p)
add_reference_arg(p)
add_verbose_arg(p)
return p
def _build_arg_parser():
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('in_tractograms',
metavar='INPUT_FILES',
nargs='+',
help='The list of files that contain the ' +
'streamlines to operate on.')
p.add_argument('out_tractogram',
metavar='OUTPUT_FILE',
help='The file where the remaining streamlines '
'are saved.')
p.add_argument('--precision',
'-p',
metavar='NBR_OF_DECIMALS',
type=int,
default=4,
help='Precision used to compare streamlines [%(default)s].')
p.add_argument('--robust',
'-r',
action='store_true',
help='Use version robust to small translation/rotation.')
p.add_argument('--no_metadata',
'-n',
action='store_true',
help='Strip the streamline metadata from the output.')
p.add_argument('--fake_metadata',
action='store_true',
help='Skip the metadata verification, create fake metadata '
'if missing, can lead to unexpected behavior.')
p.add_argument('--save_indices',
'-s',
metavar='OUT_INDEX_FILE',
help='Save the streamline indices to the supplied '
'json file.')
p.add_argument('--ignore_invalid',
action='store_true',
help='If set, does not crash because of invalid '
'streamlines.')
add_json_args(p)
add_reference_arg(p)
add_verbose_arg(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_bundle', help='Fiber bundle file.')
add_reference_arg(p)
add_json_args(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=__doc__)
p.add_argument('in_tractogram', help='Path of the input tractogram file.')
p.add_argument('out_tractogram',
help='Path of the output tractogram file.')
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',
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.')
p.add_argument('--display_counts',
action='store_true',
help='Print streamline count before and after filtering')
add_reference_arg(p)
add_verbose_arg(p)
add_overwrite_arg(p)
add_json_args(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
epilog=EPILOG,
description=__doc__)
p.add_argument('in_tractogram', help='Path of the input tractogram file.')
p.add_argument('in_wmparc',
help='Path of the white matter parcellation atlas\n' +
'(.nii or .nii.gz)')
p.add_argument('out_path', help='Path to the output files.')
p.add_argument('--minL',
default=0.,
type=float,
help='Minimum length of streamlines, in mm. [%(default)s]')
p.add_argument('--maxL',
default=np.inf,
type=float,
help='Maximum length of streamlines, in mm. [%(default)s]')
p.add_argument('-a',
dest='angle',
default=np.inf,
type=float,
help='Maximum looping (or turning) angle of\n' +
'a streamline, in degrees. [%(default)s]')
p.add_argument('--csf_bin',
help='Allow CSF endings filtering with this binary\n' +
'mask instead of using the atlas (.nii or .nii.gz)')
p.add_argument('--ctx_dilation_radius',
type=float,
default=0.,
help='Cortical labels dilation radius, in mm.\n' +
' [%(default)s]')
p.add_argument('--save_intermediate_tractograms',
action='store_true',
help='Save accepted and discarded streamlines\n' +
' after each step.')
p.add_argument('--save_volumes',
action='store_true',
help='Save volumetric images (e.g. binarised label\n' +
' images, etc) in the filtering process.')
p.add_argument('--save_counts',
action='store_true',
help='Save the streamline counts to a file (.json)')
p.add_argument('--no_empty',
action='store_true',
help='Do not write file if there is no streamlines.')
add_reference_arg(p)
add_verbose_arg(p)
add_overwrite_arg(p)
add_json_args(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('voxel_label_map', help='Fiber bundle file.')
p.add_argument('bundle_name', help='Bundle name.')
add_json_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_bundles',
nargs='+',
help='List of tractography files supported by nibabel.')
p.add_argument('in_labels',
nargs='+',
help='List of labels maps that matches the bundles.')
p.add_argument('--fitting_func',
choices=['lin_up', 'lin_down', 'exp', 'inv', 'log'],
default=None,
help='Function to weigh points using their distance.'
'\n[Default: %(default)s]')
p2 = p.add_argument_group(title='Visualization options')
p3 = p2.add_mutually_exclusive_group()
p3.add_argument('--show_rendering',
action='store_true',
help='Display VTK window (optional).')
p3.add_argument('--save_rendering',
metavar='OUT_FOLDER',
help='Save VTK render in the specified folder (optional)')
p2.add_argument('--wireframe',
action='store_true',
help='Use wireframe for the tube rendering.')
p2.add_argument('--error_coloring',
action='store_true',
help='Use the fitting error to color the tube.')
p2.add_argument('--width',
type=float,
default=0.2,
help='Width of tubes or lines representing streamlines'
'\n[Default: %(default)s]')
p2.add_argument('--opacity',
type=float,
default=0.2,
help='Opacity for the streamlines rendered with the tube.'
'\n[Default: %(default)s]')
p2.add_argument('--background',
metavar=('R', 'G', 'B'),
nargs=3,
default=[1, 1, 1],
type=parser_color_type,
help='RBG values [0, 255] of the color of the background.'
'\n[Default: %(default)s]')
add_reference_arg(p)
add_json_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_bundles', nargs='+', help='Path of the input bundles.')
p.add_argument('out_json', help='Path of the output file.')
add_reference_arg(p)
add_processes_arg(p)
add_json_args(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description='Compute streamlines min, mean and max length, as well as '
'standard deviation of length in mm.',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
p.add_argument('in_bundle', help='Fiber bundle file.')
add_reference_arg(p)
add_json_args(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_matrices', nargs='+',
help='Path of the input matricies.')
p.add_argument('out_json',
help='Path of the output json file.')
p.add_argument('--single_compare',
help='Compare inputs to this single file.')
add_json_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_bundles', nargs='+', help='Path of the input bundles.')
p.add_argument('out_json', help='Path of the output file.')
p.add_argument('--group_statistics',
action='store_true',
help='Show average measures \n'
'[%(default)s].')
add_reference_arg(p)
add_processes_arg(p)
add_json_args(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=__doc__)
p.add_argument('in_json',
nargs='+',
help='List of json files to merge (.json).')
p.add_argument('out_json', help='Output json file (.json).')
p.add_argument('--keep_separate',
action='store_true',
help='Merge entries as separate keys.')
add_json_args(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
p.add_argument("in_tractogram", help="Input tractogram to score")
p.add_argument("gt_bundles",
nargs="+",
help="Bundles ground truth (.[trk|.tck|.nii|.nii.gz]).")
g = p.add_argument_group("ROIs")
g.add_argument("--gt_endpoints",
nargs="+",
help="Bundles endpoints, both bundle's ROIs\
(.nii or .nii.gz).")
g.add_argument("--gt_tails",
nargs="+",
help="Bundles tails, bundle's first ROI(.nii or .nii.gz).")
g.add_argument("--gt_heads",
nargs="+",
help="Bundles heads, bundle's second ROI(.nii or .nii.gz).")
p.add_argument("--dilate_endpoints",
metavar="NB_PASS",
default=1,
type=int,
help="Dilate masks n-times.")
p.add_argument("--gt_config",
metavar="FILE",
help=".json dict to specify bundles streamlines min, \
max length and max angles.")
p.add_argument("--out_dir", default="gt_out/", help="Output directory")
p.add_argument("--wrong_path_as_separate",
action="store_true",
help="Separates streamlines that go outside of the ground \
truth mask from true connections, outputs as \
*_wpc.[tck|trk].")
p.add_argument("--remove_invalid",
action="store_true",
help="Remove invalid streamlines before scoring.")
add_json_args(p)
add_overwrite_arg(p)
add_reference_arg(p)
add_verbose_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_bundle', help='Fiber bundle filename.')
p.add_argument('endpoints_map_head',
help='Output endpoints map head filename.')
p.add_argument('endpoints_map_tail',
help='Output endpoints map tail filename.')
p.add_argument('--swap',
action='store_true',
help='Swap head<->tail convention. '
'Can be useful when the reference is not in RAS.')
add_json_args(p)
add_reference_arg(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
p.add_argument('in_bundle',
help='Fiber bundle file to compute statistics on')
p.add_argument('metrics', nargs='+',
help='Nifti file to compute statistics on. Probably some '
'tractometry measure(s) such as FA, MD, RD, ...')
p.add_argument('--density_weighting',
action='store_true',
help='If set, weight statistics by the number of '
'fibers passing through each voxel.')
add_reference_arg(p)
add_json_args(p)
return p
