Fibre orientation atlas guided rapid segmentation of white matter tracts.

"a dataset of 16 healthy adult hardi acquisitions ('eeg fmri and noddi dataset'; clayden & deligianni available online at osf io/94c5t) was used in the creation of reference bundles for developing the atlas.; the recently released tractoinferno database (v1 1 1 available at https://openneuro org/datasets/ds003900/versions/1 1 1 ) (poulin et al ) created for the training of machine learning tractography approaches contains diffusion and t1-weighted mri scans for 284 subjects pooled from several studies accompanied by reference streamline tractography reconstructions.; tract orientation atlases (and corresponding training streamlines) for the af cst ifof and or are openly available for non-commercial use: https://doi org/10 5281/zenodo 10149873 .; this study utilised data from the human connectome project (hcp) and tractoinferno database publicly available at https://www humanconnectome org/study/hcp-young-adult/document/1200-subjects-data-release and https://openneuro org/datasets/ds003900 respectively. processing and analysis pipelines for the two openly available datasets are available at https://github com/fionaeyoung/pipelines .; data availability statement scripts for running tractfinder and generating custom tract atlases are available at https://github com/fionaeyoung/tractfinder . data s1."

"users can generate custom atlases from a set of training streamlines using the code available at https://github com/fionaeyoung/tractfinder .; tractfinder is available as an external mrtrix3 module at https://github com/fionaeyoung/tractfinder .; processing and analysis pipelines for the two openly available datasets are available at https://github com/fionaeyoung/pipelines .; tractseg is a deep learning tract segmentation model which produces volumetric segmentations for 72 tracts directly from fibre orientation distribution peak directions (tractseg v2 3-2 6 available at https://github com/mic-dkfz/tractseg ).; however users can easily construct additional custom atlases using only 10-20 training samples and code to do so is available online: https://github com/fionaeyoung/tractfinder .; data availability statement scripts for running tractfinder and generating custom tract atlases are available at https://github com/fionaeyoung/tractfinder .; processing pipelines and code scripts used to compare segmentations and produce summary figures are available at https://github com/fionaeyoung/pipelines ."

"CONFLICT OF INTEREST STATEMENT The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Fiona Young, Jonathan D. Clayden, Kristian Aquilina and Chris A. Clark have patent pending to UCL Business PLC. All other authors declare no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper."

"FUNDING INFORMATION This work is supported by the EPSRC‐funded UCL Centre for Doctoral Training in Intelligent, Integrated Imaging in Healthcare (i4health) (EP/S021930/1). In addition, all research at Great Ormond Street Hospital NHS Foundation Trust and UCL Great Ormond Street Institute of Child Health is made possible by the Department of Health's NIHR‐funded Great Ormond Street Hospital Biomedical Research Centre. Some of the NHNN data acquisition was funded by a grant provided by the NIHR UCL/UCLH Comprehensive Biomedical Research Centre (BRC) (Project Award reference 74). LM was supported, at the time of NHNN data acquisition, by the NIHR UCL/UCLH BRC. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health."