Citations
General citation for DSI Studio and Fiber Data Hub
When citing DSI Studio, cite the 2025 Nature Methods paper and report the exact DSI Studio release used for the analysis. The version family (Sun, Hou, Chen, etc.) may be included as additional information, but it should not replace the exact release date.
Recommended citation
Yeh FC. DSI Studio: an integrated tractography platform and fiber data hub for accelerating brain research. Nature Methods. 2025;22(8):1617-1619. doi:10.1038/s41592-025-02762-8.
Example methods statement
The analysis was conducted using DSI Studio (Yeh, 2025), version YYYY.MM.DD (Sun).
For reproducibility, keep a copy of the DSI Studio version used for each project and report relevant reconstruction/tracking parameters in the methods.
Method-specific citations
Use the corresponding method paper when a study relies substantially on one of the following methods.
Differential tractography and SRC quality control
Differential tractography maps pathway segments showing changes in diffusion measurements. The same paper introduced neighboring-DWI correlation as a diffusion-data quality-control measure used by DSI Studio.
Yeh FC, Zaydan IM, Suski VR, Lacomis D, Richardson RM, Maroon JC, et al. Differential tractography as a track-based biomarker for neuronal injury. NeuroImage. 2019;202:116131. doi:10.1016/j.neuroimage.2019.116131.
Correlational tractography / tractography methodology
Yeh FC, Irimia A, Bastos DCA, Golby AJ. Tractography methods and findings in brain tumors and traumatic brain injury. NeuroImage. 2021;245:118651. doi:10.1016/j.neuroimage.2021.118651.
Group connectometry
Connectometry tests statistical associations in local connectome measurements and uses permutation testing for inference.
Yeh FC, Badre D, Verstynen T. Connectometry: A statistical approach harnessing the analytical potential of the local connectome. NeuroImage. 2016;125:162-171. doi:10.1016/j.neuroimage.2015.10.053.
Tract-to-region connectome
Yeh FC. Population-based tract-to-region connectome of the human brain and its hierarchical topology. Nature Communications. 2022;13:4933. doi:10.1038/s41467-022-32595-4.
Shape analysis and augmented fiber tracking
The same study describes tractography shape metrics and the augmented fiber-tracking strategies used to improve the reproducibility of deterministic tracking.
Yeh FC. Shape analysis of the human association pathways. NeuroImage. 2020;223:117329. doi:10.1016/j.neuroimage.2020.117329.
Topology-informed pruning (TIP)
Yeh FC, Panesar S, Barrios J, Fernandes D, Abhinav K, Meola A, Fernandez-Miranda JC. Automatic Removal of False Connections in Diffusion MRI Tractography Using Topology-Informed Pruning (TIP). Neurotherapeutics. 2019;16(1):52-58. doi:10.1007/s13311-018-0663-y.
Population-averaged tractography atlas
This paper describes the HCP842 population-averaged structural-connectome/tractography atlas and its network topology.
Yeh FC, Panesar S, Fernandes D, Meola A, Yoshino M, Fernandez-Miranda JC, et al. Population-averaged atlas of the macroscale human structural connectome and its network topology. NeuroImage. 2018;178:57-68. doi:10.1016/j.neuroimage.2018.05.027.
Restricted diffusion imaging (RDI)
Yeh FC, Liu L, Hitchens TK, Wu YL. Mapping immune cell infiltration using restricted diffusion MRI. Magnetic Resonance in Medicine. 2017;77(2):603-612. doi:10.1002/mrm.26143.
Local connectome fingerprint
Yeh FC, Vettel JM, Singh A, Poczos B, Grafton ST, Erickson KI, et al. Quantifying differences and similarities in whole-brain white matter architecture using local connectome fingerprints. PLoS Computational Biology. 2016;12(11):e1005203. doi:10.1371/journal.pcbi.1005203.
Individual connectometry
Yeh FC, Tang PF, Tseng WYI. Diffusion MRI connectometry automatically reveals affected fiber pathways in individuals with chronic stroke. NeuroImage: Clinical. 2013;2:912-921. doi:10.1016/j.nicl.2013.06.014.
Deterministic diffusion fiber tracking and quantitative anisotropy
Yeh FC, Verstynen TD, Wang Y, Fernandez-Miranda JC, Tseng WYI. Deterministic diffusion fiber tracking improved by quantitative anisotropy. PLoS ONE. 2013;8(11):e80713. doi:10.1371/journal.pone.0080713.
Q-space diffeomorphic reconstruction (QSDR)
Yeh FC, Tseng WYI. NTU-90: a high angular resolution brain atlas constructed by q-space diffeomorphic reconstruction. NeuroImage. 2011;58(1):91-99. doi:10.1016/j.neuroimage.2011.06.021.
Generalized q-sampling imaging (GQI)
Yeh FC, Wedeen VJ, Tseng WYI. Generalized q-sampling imaging. IEEE Transactions on Medical Imaging. 2010;29(9):1626-1635. doi:10.1109/TMI.2010.2045126.
Publications using DSI Studio
A broader list of publications using DSI Studio is available in the publication spreadsheet.