Brain Structure and Function

, Volume 223, Issue 6, pp 2841–2858 | Cite as

When tractography meets tracer injections: a systematic study of trends and variation sources of diffusion-based connectivity

  • Dogu Baran Aydogan
  • Russell Jacobs
  • Stephanie Dulawa
  • Summer L. Thompson
  • Maite Christi Francois
  • Arthur W. Toga
  • Hongwei Dong
  • James A. Knowles
  • Yonggang Shi
Original Article


Tractography is a powerful technique capable of non-invasively reconstructing the structural connections in the brain using diffusion MRI images, but the validation of tractograms is challenging due to lack of ground truth. Owing to recent developments in mapping the mouse brain connectome, high-resolution tracer injection-based axonal projection maps have been created and quickly adopted for the validation of tractography. Previous studies using tracer injections mainly focused on investigating the match in projections and optimal tractography protocols. Being a complicated technique, however, tractography relies on multiple stages of operations and parameters. These factors introduce large variabilities in tractograms, hindering the optimization of protocols and making the interpretation of results difficult. Based on this observation, in contrast to previous studies, in this work we focused on quantifying and ranking the amount of performance variation introduced by these factors. For this purpose, we performed over a million tractography experiments and studied the variability across different subjects, injections, anatomical constraints and tractography parameters. By using N-way ANOVA analysis, we show that all tractography parameters are significant and importantly performance variations with respect to the differences in subjects are comparable to the variations due to tractography parameters, which strongly underlines the importance of fully documenting the tractography protocols in scientific experiments. We also quantitatively show that inclusion of anatomical constraints is the most significant factor for improving tractography performance. Although this critical factor helps reduce false positives, our analysis indicates that anatomy-informed tractography still fails to capture a large portion of axonal projections.


Tractography Validation ANOVA Mouse Connectome 



This work was supported by the National Institute of Health (NIH) under Grants R01EB022744, K01EB013633, P41EB015922, P50AG005142, U01EY025864 and U01AG051218.


The study was funded by the National Institute of Health (NIH) (Grant numbers: R01EB022744, K01EB013633, P41EB015922, P50AG005142, U01EY025864, U01AG051218).

Compliance with ethical standards

Statement on the welfare of animals

All procedures performed in studies involving animals were in accordance with the ethical standards of the institution or practice at which the studies were conducted.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

429_2018_1663_MOESM1_ESM.docx (4.4 mb)
Supplementary material 1 (DOCX 4546 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Dogu Baran Aydogan
    • 1
  • Russell Jacobs
    • 2
  • Stephanie Dulawa
    • 3
  • Summer L. Thompson
    • 3
    • 4
  • Maite Christi Francois
    • 5
  • Arthur W. Toga
    • 1
  • Hongwei Dong
    • 1
  • James A. Knowles
    • 5
  • Yonggang Shi
    • 1
  1. 1.Laboratory of Neuro Imaging (LONI), USC Stevens Neuroimaging and Informatics Institute, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUSA
  2. 2.Department of Physiology and Biophysics, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUSA
  3. 3.Department of PsychiatryUniversity of California at San DiegoSan DiegoUSA
  4. 4.Committee on NeurobiologyUniversity of ChicagoChicagoUSA
  5. 5.Department of Psychiatry, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUSA

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