Overview
Accurate lesion segmentation is critical for stroke rehabilitation research for both quantification of lesion burden and accurate image processing. Current automated lesion segmentation methods for T1-weighted MRIs lack the accuracy to be used reliably in research. Manual segmentation remains the gold standard, but it is time-consuming and requires significant neuroanatomical expertise. We previously release large, open-source datasets of stroke T1-weighted MRIs and manually segmented lesion masks (ATLAS v2.1, N=955; ATLAS v1.2, N=304) to encourage the development of better segmentation algorithms. However, most methods developed with ATLAS v2.1 and v1.2 are not publicly accessible or have been overfitted to the data, resulting in algorithms with poor performance on new data. Here we present ATLAS v3.0 (n=1453), a revision to a larger dataset of stroke T1-weighted MRIs and lesion masks that comes in two forms: (1) minimally processed, and (2) fully normalized. Algorithm development using this larger sample should lead to more robust solutions, and the hidden test data allows for unbiased performance evaluation via web-based challenges. We anticipate that ATLAS v3.0 will lead to the development of improved lesion segmentation algorithms, facilitating large-scale stroke research.
The dataset includes:
- 1453 T1-weighted MRI scans
- 1453 Corresponding binary masks, corresponding to stroke lesion
- 1453 Metadata csv files consisting of days since stroke onset, chronicity, site, and ATLAS 2.0 dataset assignment (Training vs Testing vs New for ATLAS3)
Release Download
Note: In order to obtain the password needed to access the data, you must agree to the Terms of Use specified on this page and complete a brief Google form. After completing the Google Form, your completed application will be reviewed, and an encryption code to access the data will then be given to you. Please note that this process should be completed for each individual accessing the data, and the encryption code should not be shared with others.
Release Notes
Release R1.2: N=304 (N=229 Preprocessed)
Release R2.0: N=955. Dataset now includes training and testing data. Data has been reorganized to BIDS derivatives format.
Release R2.1: N=955. Dataset now includes previously hidden masks for the testing set from Release 2.0. Two versions of the data are now also available: (1) minimally preprocessed and (2) fully normalized data.
Release R3.0: N=1453. Dataset now includes 498 new scans. A metadata csv has been added for each scan to indicate days post stroke or chronicity (when available).
Data Descriptor Manuscript for R3.0
Data Descriptor Manuscript for R2.0
Click here to access the printed version of the R2.0 data descriptor in Scientific Data.
Data Descriptor Manuscript for R1.2
Click here to access the printed version of the data descriptor in Scientific Data.
Authors and Affiliations (for R3.0)
Stuti Chakraborty, BS1*, Mahir H. Khan, PhD2*, Ezequiel de la Rosa, PhD3, Octavio Marin-Pardo, PhD1, Bethany P. Tavenner, BS4, John Absher, MD5, Tim-Mathis Beutel, MD6, Felix Bitzer, MD6, Leonardo Bonilha, MD, PhD5, Michael R. Borich, PhD7, Lara A. Boyd, PhD8, Amy G. Brodtmann, PhD, MD9,10, Truman R. Brown, PhD11,12, Cathrin M. Buetefisch, PhD, MD13, Amelia Cain, DPT14, Mariano Cabezas, PhD15, Jessica M. Cassidy, PhD, PT16, Ashley Catchpole, OTD1, Steven C. Cramer, MD17,18, Julian Deseö, MS3,19, Michael A. Dimyan, MD20, Martin Domin, PhD21, Adrienne N. Dula, PhD22, Margarita Alethea Eidsness, MS6, Elsa R. Ermer, PhD23, Jennifer K. Ferris, PhD24, Wuwei Feng, MD25, Emily E. Fokas26, Niko H. Fullmer, BA27, Fatemeh Geranmayeh, PhD, MD28, Adrià Bermudo-Gallaguet, PhD29,30,31, Makayla Gibson, PhD32, Chris M. Gregory, PhD, PT33, Jeanette R. Gumarang, BSN, MSN, RN27, Colleen A. Hanlon, PhD34, Leticia Hayes, BSN, RN26, Christina Holl, DPT14, Brenton Hordacre, PhD35, Abhishek Jaywant, PhD36, Neda Jahanshad, PhD37, Steven A. Kautz, PhD38, Mohamed Salah Khlif, PhD9, Jan S. Kirschke, MD6, Amisha Kumar, BSc38, Kristan A. Leech, PhD14, Jingchun Liu, MD39, Martin Lotze, PhD21, Bradley J. MacIntosh, PhD40, Maria Mataró, PhD29,30,31, Bjoern Menze, PhD3, Feroze Mohamed, PhD, MS41, Kyle Nishimura, OTD, OTR/L42, Ava Pimentel, BS43, Fabrizio Piras, PhD44, Mauricio Reyes, PhD45,46, Andrew D. Robertson, PhD47, Christopher Rorden, PhD32, Emily R. Rosario, PhD27, Heidi M. Schambra, MD26,48, Lena Schmitzer, MD6, Nicolas Schweighofer, PhD14, Na Jin Seo, PhD33, Grace C. Song, MA1, Surjo R. Soekadar, MD49, Ruisheng Su, PhD50, Myriam Taga, PhD51, Gregory T. Thielman, PT, MSPT, EdD52, Sophia I. Thomopoulos, BA53, Paul M. Thompson, PhD53, Daniela Vecchio, PhD44, Steven J. Warach, PhD, MD22, Lars T. Westlye, PhD54,55, Benedikt Wiestler, MD56,57, Carolee J. Winstein, PhD14, George F. Wittenberg, PhD, MD58,59, Kristin A. Wong, MD22,60, Chunshui Yu, MD39, Cansu Yalcin, MS15, Zhong Sheng Zheng, PhD61, Sook-Lei Liew, PhD, OTR/L1,14,37,53,62
1. Chan Division of Occupational Science and Occupational Therapy, University of Southern California, Los Angeles, CA, USA.
2. Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA.
3. Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
4. Department of Psychology, University of California, Riverside, Riverside, CA, USA.
5. University of South Carolina School of Medicine, Columbia, SC, USA.
6. Department of Neuroradiology, TUM University Hospital, Munich, Germany.
7. Department of Rehabilitation Medicine, Emory University School of Medicine, Atlanta, GA, USA.
8. Department of Physical Therapy, University of British Columbia, Vancouver, BC, Canada.
9. Department of Neuroscience, School of Translational Medicine, Monash University, Melbourne, Victoria, Australia.
10. Department of Neurology, Royal Melbourne Hospital, University of Melbourne, Melbourne, VIC, Australia.
11. Department of Radiology, Medical University of South Carolina, Charleston, SC, USA.
12. Ralph H. Johnson VA Health Care System, Charleston, SC, USA.
13. Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
14. Division of Biokinesiology and Physical Therapy, University of Southern California, Los Angeles, CA, USA.
15. Research Institute of Computer Vision and Robotics (VICOROB), University of Girona, Girona, Spain.
16. Department of Physical Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
17. Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
18. California Rehabilitation Institute, Los Angeles, CA, USA.
19. Department of Neurology and Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland.
20. Food and Drug Administration, Baltimore, MD, USA.
21. Functional Imaging Unit, Department for Radiology and Neuroradiology, University of Greifswald, Greifswald, Germany.
22. Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA.
23. Henry M. Jackson Foundation for the Advancement of Military Medicine, Columbia, MD, USA.
24. Gerontology Research Center, Simon Fraser University, Vancouver, British Columbia, Canada.
25. Department of Neurology, Duke University School of Medicine, Durham, NC, USA.
26. Department of Neurology, NYU Grossman School of Medicine, New York, NY, USA.
27. Casa Colina Hospital and Centers for Healthcare Research Institute, Pomona, CA, USA.
28. Department of Brain Sciences, Imperial College London, London, UK.
29. Departament de Psicologia Clínica i Psicobiologia, Facultat de Psicologia, Universitat de Barcelona, Passeig de la Vall d'Hebron, Barcelona, Spain.
30. Institut de Neurociències, Universitat de Barcelona, Passeig de la Vall d'Hebron, Barcelona, Spain.
31. Institut de Recerca Sant Joan de Déu, Santa Rosa, Esplugues de Llobregat, Spain.
32. Department of Psychology, University of South Carolina, Columbia, SC, USA.
33. Department of Health Sciences and Research, Medical University of South Carolina, Charleston, SC, USA.
34. BrainsWay Inc., USA.
35. Innovation, Implementation and Clinical Translation in Health, Allied Health and Human Performance, Adelaide University, Adelaide, Australia.
36. Department of Neuropsychology in Psychiatry, Weill Cornell Medical College, New York, NY, USA.
37. Laboratory of Brain eScience, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
38. Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA.
39. Department of Radiology, Tianjin Medical University General Hospital, Tianjin, China.
40. Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
41. Jefferson Integrated Magnetic Resonance Imaging Center, Department of Radiology, Thomas Jefferson University, Philadelphia, PA, USA.
42. University of Southern California Arcadia Hospital, Los Angeles, CA, USA.
43. California State University, Fullerton, Fullerton, CA, USA.
44. Clinical Neuroscience and Neurorehabilitation, IRCCS Santa Lucia Foundation, Rome, Italy.
45. ARTORG Center for Biomedical Engineering Research, University of Bern, Bern, Switzerland.
46. Department of Radiation Oncology, University Hospital Bern, University of Bern, Bern, Switzerland.
47. Department of Kinesiology, University of Waterloo, Waterloo, Ontario, Canada.
48. Department of Rehabilitation Medicine, NYU Grossman School of Medicine, New York, NY, USA.
49. Clinical Neurotechnology Laboratory, Department of Psychiatry and Neurosciences (CCM), Charité – Universitätsmedizin Berlin, Berlin, Germany.
50. Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
51. NeuroPlastix, Zug, Switzerland.
52. Department of Physical Therapy and Neuroscience, Saint Joseph's University, Philadelphia, PA, USA.
53. Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
54. Department of Psychology, University of Oslo, Oslo, Norway.
55. Center for Precision Psychiatry, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.
56. AI for Image-Guided Diagnosis and Therapy, School of Medicine and Health, Technical University of Munich, Munich, Germany.
57. Institute of Neuroradiology, TUM University Hospital, Munich, Germany.
58. Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA.
59. Department of Veterans Affairs Geriatrics Research, Education and Clinical Center, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA.
60. Department of Physical Medicine and Rehabilitation, Dell Medical School, The University of Texas at Austin, Austin, TX, USA.
61. Institute for Advanced Consciousness Studies, Santa Monica, CA, USA.
62. Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
Corresponding author: Sook-Lei Liew (sliew@usc.edu)
*Denotes equal contributions
FAQs
Q: Is there information on the training protocol for lesion annotations?
A: Yes! We have included this information in the latest preprint. A narrated walkthrough of the training material can be accessed on our YouTube channel. Our complete lesion tracing guidance document along with the neuroanatomy training slides can be accessed on GitHub. The corresponding imaging and mask data are divided into two sets, one for each stage of training, and can be downloaded here: [Set 1] [Set 2].
Acknowledgements
The archiving of this dataset was specifically supported by the NIH-funded Center for Large Data Research and Data Sharing in Rehabilitation (CLDR) under a Category 2 Pilot Grant (P2CHD06570), as well as NIH RF1NS115845, NIH P50HD118603, NIH R01NS115845, NIH K01HD091283.