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Update citation for RBx -> BundleSeg #738

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Aug 28, 2023
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Merged

Update citation for RBx -> BundleSeg #738

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2 changes: 1 addition & 1 deletion scilpy/segment/streamlines.py
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Original file line number Diff line number Diff line change
Expand Up @@ -114,7 +114,7 @@ def filter_grid_roi(sft, mask, filter_type, is_exclude, filter_distance=0):
mask : numpy.ndarray
Binary mask in which the streamlines should pass.
filter_type: str
One of the 3 following choices, 'any', 'all', 'either_end', 'both_ends'.
One of the 4 following choices, 'any', 'all', 'either_end', 'both_ends'.
is_exclude: bool
Value to indicate if the ROI is an AND (false) or a NOT (true).
Returns
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17 changes: 7 additions & 10 deletions scripts/scil_recognize_multi_bundles.py
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Expand Up @@ -2,7 +2,7 @@
# -*- coding: utf-8 -*-

"""
Compute RecobundlesX (multi-atlas & multi-parameters).
Compute BundleSeg & supports multi-atlas & multi-parameters (RBx-like).
The model needs to be cleaned and lightweight.
Transform should come from ANTs: (using the --inverse flag)
AntsRegistrationSyNQuick.sh -d 3 -m MODEL_REF -f SUBJ_REF
Expand All @@ -13,7 +13,7 @@

The number of folders inside 'models_directories' will increase the number of
runs. Each folder is considered like an atlas and bundles inside will initiate
more Recobundle executions. The more atlases you have, the more robust the
more BundleSeg executions. The more atlases you have, the more robust the
recognition will be.

--minimal_vote_ratio is a value between 0 and 1. If you have 5 input model
Expand Down Expand Up @@ -44,14 +44,9 @@
from scilpy.segment.voting_scheme import VotingScheme

EPILOG = """
[1] Garyfallidis, Eleftherios, et al. "Recognition of white matter bundles using
local and global streamline-based registration and clustering."
NeuroImage (2018)
[2] St-Onge, Etienne, Eleftherios Garyfallidis, and D. Louis Collins.
"Fast Streamline Search: An Exact Technique for Diffusion MRI Tractography."
Neuroinformatics (2022)
[3] Rheault, François. "Analyse et reconstruction de faisceaux de la matière
blanche." Computer Science. Université de Sherbrooke (2020).
[1] Etienne St-Onge, Kurt Schilling, Francois Rheault, "BundleSeg: A versatile,
reliable and reproducible approach to white matter bundle segmentation.",
arXiv, 2308.10958 (2023)
"""


Expand Down Expand Up @@ -132,6 +127,8 @@ def main():
with open(args.in_config_file) as json_data:
config = json.load(json_data)

# For code simplicity, it is still RecobundlesX class and all, but
# the last pruning step was modified to be in line with BundleSeg.
voting = VotingScheme(config, args.in_models_directories,
transfo, args.out_dir,
minimal_vote_ratio=args.minimal_vote_ratio)
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