Multi-atlas bundle segmentation This data is made to be used with the following script: https://github.com/scilus/scilpy/blob/master/scripts/scil_recognize_multi_bundles.py This script is in fact a multi-atlas, multi-parameters version of *Garyfallidis et al. (2018)* with labels fusions. We name this algorithm RecobundlesX. Garyfallidis, Eleftherios, et al. "Recognition of white matter bundles using local and global streamline-based registration and clustering." _NeuroImage_ 170 (2018): 283-295. Usage Here is an example (for more details use scil_recognize_multi_bundles.py -h) : antsRegistrationSyNQuick.sh -d 3 -f ${T1} -m mni_masked.nii.gz -t a -n 4 scil_recognize_multi_bundles.py ${TRACTOGRAM} default_config.json atlas/*/ output0GenericAffine.mat --out_dir ${OUTPUT_DIR}/ --log_level DEBUG --multi_parameters 9 --minimal_vote 0.5 --tractogram_clustering 10 12 --processes 8 --seeds 0 --inverse -f Notes on bundles - AC and PC were added mostly in case the atlas is used for lesion-mapping or figures. Likely, segmentation won't produce good results. This is mostly due to difficult tracking for these bundles. - The CC are split for each lobe. However, for technical consideration, the frontal portion was split in two to facilitate clustering and segmentation. For the same reason, the portion fanning to the pre/post central gyri were separated. - The streamlines present in the CC are homotopic, Recobundles will allow for variation and thus lead to 'some' heterotopy. However, it is expected that the results will be mostly homotopic. - CG has 3 possible endpoint locations. However, the full extent of the tail is difficult to track and is often missing. - FPT and POPT should terminate in the pons. However, to fully capture candidate streamlines and improve segmentation quality even streamlines reaching down the brainstem are selected. - PYT should reach down the brainstem. For similar reasons to the FPT/POPT, streamlines ending in the pons are selected. - OR_ML will most likely have difficulty capturing the full ML. However, this is often due to difficult tracking. - The cerebellum is often cut due to acquisition FOV. In such a case, all projection bundles will be more difficult to recognize and most cerebellum bundles will be missing (ICP, MCP, SCP). # Acronym AC - Anterior commisures AF - Arcuate fasciculus CC_Fr_1 - Corpus callosum, Frontal lobe CC_Fr_2 - Corpus callosum, Frontal lobe CC_Oc - Corpus callosum, Occipital lobe CC_Pa - Corpus callosum, Parietal lobe CC_Pr_Po - Corpus callosum, Pre/Post central gyri CC_Te - Corpus callosum, Temporal lobe CG - Cingulum FAT - Frontal aslant tracts FPT - Fronto-pontine tracts FX - Fornix ICP - Inferior cerebellar peduncle IFOF - Inferior fronto-occipital fasciculus ILF - Inferior longitudinal fasciculus MCP - Middle cerebellar peduncle MdLF - Middle longitudinal fascicle OR_ML - Optic radiation and Meyer's loop PC - Posterior commisures POPT - parieto-occipito pontine tracts PYT - Pyramidal tracts SCP - Superior cerebellar peduncle SLF - Superior longitudinal fasciculus UF - Uncinate fasciculus