Citations
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General citation for DSI Studio or Fiber Data Hub
When citing DSI Studio, to ensure reproducibility, please reference the 2025 Nature Methods paper (Yeh, 2025) and additionally specify the software version (Hou or Chen), the access date, and the download source.
The analysis was conducted using DSI Studio (Yeh, 2025), the Hou version (accessed [Date], http://dsi-studio.labsolver.org).
Yeh, Fang-Cheng. "DSI Studio: an integrated tractography platform and fiber data hub for accelerating brain research." Nat Methods (2025). https://doi.org/10.1038/s41592-025-02762-8
Citations for specific methods
Reviewers may sometimes question the reliability of methods implemented in DSI Studio. The following references provide validation and testing to address such concerns.
- Tracto-to-region connectome (2022): This study constructs a population-based probablistic tractography atlas and its associated tract-to-region connectome.
Yeh, Fang-Cheng. "Population-based tract-to-region connectome of the human brain and its hierarchical topology." Nat Commun 13, 4933 (2022). https://doi.org/10.1038/s41467-022-32595-4 - Shape Analysis (2020): Shape analysis is a morphology based quantification of tractography.
Yeh, Fang-Cheng. "Shape analysis of the human association pathways." Neuroimage 223 (2020): 117329. - Augmented fiber tracking (2020): The “augmented fiber tracking” are three strategies used to boost reproducibility of deterministic fiber tracking.
Yeh, Fang-Cheng. "Shape analysis of the human association pathways." Neuroimage 223 (2020): 117329. - SRC file quality control (2019): The “neighboring DWI correlation” is introduced in this study as a QC metrics for DWI.
Yeh, Fang-Cheng, et al. "Differential tractography as a track-based biomarker for neuronal injury." NeuroImage 202 (2019): 116131. - Topology informed pruning (TIP, 2019): A topology-based approach to remove false fiber trajectories.
Yeh, F. C., Panesar, S., Barrios, J., Fernandes, D., Abhinav, K., Meola, A., & Fernandez-Miranda, J. C. (2019). Automatic Removal of False Connections in Diffusion MRI Tractography Using Topology-Informed Pruning (TIP). Neurotherapeutics, 1-7. - Tractography Atlas (2018): This study provide the tractography atlas included in DSI Studio for human young adults.
Yeh, Fang-Cheng, et al. "Population-averaged atlas of the macroscale human structural connectome and its network topology." Neuroimage 178 (2018): 57-68. - Group connectometry (2016): connectometry is a statistical framework for testing the significance of correlational tractography.
Yeh, Fang-Cheng, David Badre, and Timothy Verstynen. "Connectometry: A statistical approach harnessing the analytical potential of the local connectome." NeuroImage 125 (2016): 162-171. - Restricted diffusion imaging (RDI, 2016): RDI is a model-free method that calculates the density of diffusing spins restricted within a given displacement distance.
Yeh, Fang-Cheng, Li Liu, T. Kevin Hitchens, and Yijen L. Wu, "Mapping Immune Cell Infiltration Using Restricted Diffusion MRI", Magn Reson Med. accepted, (2016) - Local connectome fingerprint (LCF, 2016): Local conectome fingerprint provides a subject-specific measurement for characterizing the white matter architectures and quantifying differences/similarity.
Yeh, F. C., Vettel, J. M., Singh, A., Poczos, B., Grafton, S. T., Erickson, K. I., ... & Verstynen, T. D. (2016). Quantifying differences and similarities in whole-brain white matter architecture using local connectome fingerprints. PLoS computational biology, 12(11), e1005203. - Individual connectometry (2013): Individual connectometry is atlas-based analysis method that tracks the deviant pathways of one individual (e.g. a patient) by comparing subject’s data with a normal population.
Yeh, Fang-Cheng, Pei-Fang Tang, and Wen-Yih Isaac Tseng. "Diffusion MRI connectometry automatically reveals affected fiber pathways in individuals with chronic stroke." NeuroImage: Clinical 2 (2013): 912-921. - Generalized deterministic tracking algorithm (2013): The fiber tracking algorithm implemented in DSI Studio is a generalized version of the deterministic tracking algorithm that uses quantitative anisotropy as the termination index.
Yeh, Fang-Cheng, et al. "Deterministic diffusion fiber tracking improved by quantitative anisotropy." (2013): e80713. PLoS ONE 8(11): e80713. doi:10.1371/journal.pone.0080713 - Q-space diffeormophic reconstruction (QSDR, 2011): QSDR is a model-free method that calculates the orientational distribution of the density of diffusing water in a standard space.
Yeh, Fang-Cheng, and Wen-Yih Isaac Tseng, "NTU-90: a high angular resolution brain atlas constructed by q-space diffeomorphic reconstruction." Neuroimage 58.1 (2011): 91-99. - Generalized q-sampling imaging (GQI, 2010): GQI is a model-free method that calculates the orientational distribution of the density of diffusing water.
Yeh, Fang-Cheng, Van Jay Wedeen, and Wen-Yih Isaac Tseng, "Generalized q-sampling imaging" Medical Imaging, IEEE Transactions on 29.9 (2010): 1626-1635.
Media coverage
New Technology Helping To Treat Veteran Brain Injuries November 9, 2012 CBS Pittsburgh
New brain imaging at Pitt gives a better picture March 2, 2012 Pittsburgh Post-Gazette
White’s the Matter: A basic guide to white matter imaging using diffusion MRI November 1, 2014 The Scientist Magazine®
Seeing the Brain’s Broken Cables August 03, 2015e Discover Magazine
Researchers Can Now ‘Fingerprint’ the Human Brain November 18, 2016 PC Magazine
Human Brain Found to Have Fingerprint! Unique Neural Connections Proven November 17, 2016 Nature World News
Your brain ‘fingerprint’ is unique enough to ID you November 16, 2016 futurity.org
Researchers develop way to ‘fingerprint’ the brain November 15, 2016 medicalexpress.com
Steeler-sponsored Chuck Noll Foundation funds first concussion research grants Feburary 22, 2018 Pittsburgh Post-Gazette
Laboratories using DSI Studio
If you would like to have your lab added/removed, please let me know (frank.yeh@gmail.com)
- Advanced Biomedical MRI Lab at National Taiwan University Hospital (http://abmri.mc.ntu.edu.tw/)
- CoAx Lab at Carnegie Mellon University (http://www.psy.cmu.edu/~coaxlab/)
- Lab of Neurocognitive Development of the Department of Psychiatry at the University of Pittsburgh Medical Center (https://lncd.pitt.edu/wp/)
- Brain Body Stress Lab at University of Pittsburgh (http://brainbodystress.pitt.edu/)
- Walt Schneider Lab at University of Pittsburgh (http://www.lrdc.pitt.edu/schneiderlab/)
- Action Lab at University of California Santa Barbara (https://labs.psych.ucsb.edu/grafton/scott/index.html)
- NeuroImaging Network (NIN), Universal Scientific Education and Research Network (USERN), Tehran, Iran (http://usern.tums.ac.ir/Group/Info/NIN)