From a02e358da3fc034718bd49cea5223975c4bc5407 Mon Sep 17 00:00:00 2001 From: frheault Date: Wed, 23 Aug 2023 09:34:09 -0400 Subject: [PATCH] Update citation --- scilpy/segment/streamlines.py | 2 +- scripts/scil_recognize_multi_bundles.py | 17 +++++++---------- 2 files changed, 8 insertions(+), 11 deletions(-) diff --git a/scilpy/segment/streamlines.py b/scilpy/segment/streamlines.py index ef5daea61..f40e36ac1 100644 --- a/scilpy/segment/streamlines.py +++ b/scilpy/segment/streamlines.py @@ -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 diff --git a/scripts/scil_recognize_multi_bundles.py b/scripts/scil_recognize_multi_bundles.py index f9ba08b64..a8b98b1a6 100755 --- a/scripts/scil_recognize_multi_bundles.py +++ b/scripts/scil_recognize_multi_bundles.py @@ -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 @@ -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 @@ -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) """ @@ -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)