XTRACT can be used to automatically extract a set of carefully dissected tracts in humans and macaques (other species to come). It can also be used to define one's own tractography protocols where all the user needs to do is to define a set of masks in standard space (e.g. MNI152).
The script was written by Shaun Warrington, Saad Jbabdi & Stamatios Sotiropoulos (based on the autoPtx tool by Marius de Groot - see https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/AutoPtx)
The HUMAN and MACAQUE tractography protocols were created by: Rogier Mars, Stamatios Sotiropoulos, Saad Jbabdi, Kathryn Bryant, Shaun Warrington, Marina Charquero-Ballester, Gwenaelle Douaud
The BABY tractography protocols were created by: Elinor Thompson, Shaun Warrington, Matteo Bastiani, Jessica Dubois, Stamatios Sotiropoulos
The MACAQUE tractography protocols were generalised across templates by: Stephania Assimopoulos, Shaun Warrington, Stamatios Sotiropoulos
The XTRACT viewer helper script was written by Shaun Warrington
The XTRACT stats helper script was written by Shaun Warrington
The XTRACT blueprint script was written by Shaun Warrington and Saad Jbabdi
The XTRACT QC helper script was written by Shaun Warrington
The XTRACT divergence script was written by Shaun Warrington and Stephania Assimopoulos
Warrington S., Bryant K., Khrapitchev A., Sallet J., Charquero-Ballester M., Douaud G., Jbabdi S., Mars R., Sotiropoulos S.N.* (2020) XTRACT - Standardised protocols for automated tractography in the human and macaque brain. NeuroImage. DOI: 10.1016/j.neuroimage.2020.116923
de Groot M., Vernooij MW. Klein S., Ikram M.A., Vos F.M., Smith S.M., Niessen W.J., Andersson J.L.R. (2013) Improving alignment in Tract-based spatial statistics: Evaluation and optimization of image registration. NeuroImage, 76(1), 400-411. DOI: 10.1016/j.neuroimage.2013.03.015
If you use the neonatal protocols, please cite:
Warrington, S., Thompson, E., Bastiani, M., Dubois, J., Baxter, L., Slater, R., Jbabdi, S., Mars, R.B., and Sotiropoulos, S.N. (2022) “Concurrent mapping of brain ontogeny and phylogeny within a common space: Standardized tractography and applications”, Science Advances, vol. 8(42), doi.org/10.1101/2022.03.03.482776
If you use the macaque protocols, please cite:
Assimopoulos, S., Warrington, S., Bryant, K.L., Pszczolkowski, S., Jbabdi S., Mars R., Sotiropoulos S.N. Generalising XTRACT tractography protocols across common macaque brain templates. Brain Struct Funct (2024). https://doi.org/10.1007/s00429-024-02760-0
For full details and usage, see the FSL wiki page: https://fsl.fmrib.ox.ac.uk/fsl/docs/#/diffusion/xtract