A large, curated, open-source stroke neuroimaging dataset to improve lesion segmentation algorithms

Sook-Lei Liew^#^{1

2}, Bethany P Lo^#³, Miranda R Donnelly³, Artemis Zavaliangos-Petropulu⁴, Jessica N Jeong³, Giuseppe Barisano^{5

6}, Alexandre Hutton³, Julia P Simon⁴, Julia M Juliano⁶, Anisha Suri⁷, Zhizhuo Wang³, Aisha Abdullah³, Jun Kim⁴, Tyler Ard⁴, Nerisa Banaj⁸, Michael R Borich⁹, Lara A Boyd¹⁰, Amy Brodtmann¹¹, Cathrin M Buetefisch^{9

12}, Lei Cao¹³, Jessica M Cassidy¹⁴, Valentina Ciullo⁸, Adriana B Conforto^{15

16}, Steven C Cramer¹⁷, Rosalia Dacosta-Aguayo¹⁸, Ezequiel de la Rosa^{19

20}, Martin Domin²¹, Adrienne N Dula²², Wuwei Feng²³, Alexandre R Franco^{13

24

25}, Fatemeh Geranmayeh²⁶, Alexandre Gramfort²⁷, Chris M Gregory²⁸, Colleen A Hanlon²⁹, Brenton G Hordacre³⁰, Steven A Kautz^{28

31}, Mohamed Salah Khlif³², Hosung Kim⁴, Jan S Kirschke³³, Jingchun Liu³⁴, Martin Lotze²¹, Bradley J MacIntosh^{35

36}, Maria Mataró^{37

38}, Feroze B Mohamed³⁹, Jan E Nordvik^{40

41}, Gilsoon Park⁵, Amy Pienta⁴², Fabrizio Piras⁸, Shane M Redman⁴², Kate P Revill⁴³, Mauricio Reyes⁴⁴, Andrew D Robertson^{45

46}, Na Jin Seo^{28

31

47}, Surjo R Soekadar⁴⁸, Gianfranco Spalletta^{8

49}, Alison Sweet⁴², Maria Telenczuk²⁷, Gregory Thielman⁵⁰, Lars T Westlye^{51

52}, Carolee J Winstein^{53

54}, George F Wittenberg^{55

56}, Kristin A Wong⁵⁷, Chunshui Yu^{34

58}

Affiliations

¹ Chan Division of Occupational Science and Occupational Therapy, University of Southern California, Los Angeles, CA, USA. sliew@usc.edu.
² Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA. sliew@usc.edu.
³ Chan Division of Occupational Science and Occupational Therapy, University of Southern California, Los Angeles, CA, USA.
⁴ Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
⁵ Laboratory of Neuroimaging, Mark and Mary Stevens Neuroimaging and Informatics Institutes, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
⁶ Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA.
⁷ Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
⁸ Laboratory of Neuropsychiatry, IRCCS Santa Lucia Foundation, Rome, Italy.
⁹ Department of Rehabilitation Medicine, Emory University School of Medicine, Atlanta, GA, USA.
¹⁰ Department of Physical Therapy & Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada.
¹¹ Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia.
¹² Department of Neurology, Emory University, Atlanta, GA, USA.
¹³ Center for the Developing Brain, Child Mind Institute, New York, NY, USA.
¹⁴ Department of Allied Health Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
¹⁵ Hospital das Clínicas, São Paulo University, Sao Paulo, SP, Brazil.
¹⁶ Hospital Israelita Albert Einstein, Sao Paulo, SP, Brazil.
¹⁷ Department of Neurology, University of California Los Angeles and California Rehabilitation Institute, Los Angeles, CA, USA.
¹⁸ Department of Psychiatry and Clinical Psychobiology, University of Barcelona, Barcelona, Spain.
¹⁹ icometrix, Leuven, Belgium.
²⁰ Department of Computer Science, Technical University of Munich, Munich, Germany.
²¹ Functional Imaging Unit, Department of Diagnostic Radiology and Neuroradiology, University of Greifswald, Greifswald, Germany.
²² Departments of Neurology and Diagnostic Medicine, Dell Medical School at The University of Texas Austin, Austin, TX, USA.
²³ Department of Neurology, Duke University School of Medicine, Durham, NC, USA.
²⁴ Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA.
²⁵ Department of Psychiatry, NYU Grossman School of Medicine, New York, NY, USA.
²⁶ Department of Brain Sciences, Imperial College London, London, UK.
²⁷ Center for Data Science, Université Paris-Saclay, Inria, Palaiseau, France.
²⁸ Department of Health Sciences & Research, Medical University of South Carolina, Charleston, SC, USA.
²⁹ Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, USA.
³⁰ Innovation, Implementation and Clinical Translation (IIMPACT) in Health, Allied Health and Human Performance, University of South Australia, Adelaide, South Australia, Australia.
³¹ Ralph H Johnson VA Medical Center, Charleston, SC, USA.
³² The Florey Institute of Neuroscience and Mental Health, Heidelberg, VIC, Australia.
³³ Neuroradiology, School of Medicine, Technical University Munich, München, Germany.
³⁴ Department of Radiology, Tianjin Medical University General Hospital, Tianjin, China.
³⁵ Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
³⁶ Hurvitz Brain Sciences Program, Toronto, Ontario, Canada.
³⁷ Department of Clinical Psychology and Psychobiology, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain.
³⁸ Institut de Recerca Sant Joan de Déu, 08950, Esplugues de Llobregat, Spain.
³⁹ Jefferson Magnetic Resonance Imaging Center, Philadelphia, PA, USA.
⁴⁰ CatoSenteret Rehabilitation Center, SON, Norway.
⁴¹ Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway.
⁴² Inter-university Consortium for Political and Social Research, University of Michigan, Ann Arbor, MI, USA.
⁴³ Facility for Education and Research in Neuroscience, Emory University, Atlanta, GA, USA.
⁴⁴ ARTORG Center for Biomedical Engineering Research, University of Bern, Bern, Switzerland.
⁴⁵ Schlegel-University of Waterloo Research Institute for Aging, University of Waterloo, Waterloo, Ontario, Canada.
⁴⁶ Canadian Partnership for Stroke Recovery, Sunnybrook Research Institute, Toronto, Ontario, Canada.
⁴⁷ Department of Rehabilitation Sciences, Medical University of South Carolina, Charleston, SC, USA.
⁴⁸ Clinical Neurotechnology Laboratory, Dept. of Psychiatry and Neurosciences (CCM), Charité - Universitätsmedizin Berlin, Berlin, Germany.
⁴⁹ Menninger Department of Psychiatry and Behavioral Sciences, Division of Neuropsychiatry, Baylor College of Medicine, Houston, TX, USA.
⁵⁰ Department of Physical Therapy and Neuroscience, Samson College of Health Sciences, St. Joseph's University, Philadelphia, PA, USA.
⁵¹ Department of Psychology, University of Oslo, Oslo, Norway.
⁵² NORMENT, Department of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.
⁵³ Division of Biokinesiology and Physical Therapy of the Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA.
⁵⁴ Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
⁵⁵ Geriatrics Research, Education and Clinical Center, HERL, Department of Veterans Affairs, Pittsburgh, PA, USA.
⁵⁶ Departments of Neurology, PM&R, RNEL, CNBC, University of Pittsburgh, Pittsburgh, PA, USA.
⁵⁷ Department of Physical Medicine & Rehabilitation, Dell Medical School, University of Texas at Austin, Austin, TX, USA.
⁵⁸ Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China.

^# Contributed equally.

PMID: 35710678
PMCID: PMC9203460
DOI: 10.1038/s41597-022-01401-7

A large, curated, open-source stroke neuroimaging dataset to improve lesion segmentation algorithms

Sook-Lei Liew et al. Sci Data. 2022.

. 2022 Jun 16;9(1):320.

doi: 10.1038/s41597-022-01401-7.

Authors

Affiliations

¹ Chan Division of Occupational Science and Occupational Therapy, University of Southern California, Los Angeles, CA, USA. sliew@usc.edu.
² Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA. sliew@usc.edu.
³ Chan Division of Occupational Science and Occupational Therapy, University of Southern California, Los Angeles, CA, USA.
⁴ Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
⁵ Laboratory of Neuroimaging, Mark and Mary Stevens Neuroimaging and Informatics Institutes, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
⁶ Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA.
⁷ Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
⁸ Laboratory of Neuropsychiatry, IRCCS Santa Lucia Foundation, Rome, Italy.
⁹ Department of Rehabilitation Medicine, Emory University School of Medicine, Atlanta, GA, USA.
¹⁰ Department of Physical Therapy & Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada.
¹¹ Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia.
¹² Department of Neurology, Emory University, Atlanta, GA, USA.
¹³ Center for the Developing Brain, Child Mind Institute, New York, NY, USA.
¹⁴ Department of Allied Health Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
¹⁵ Hospital das Clínicas, São Paulo University, Sao Paulo, SP, Brazil.
¹⁶ Hospital Israelita Albert Einstein, Sao Paulo, SP, Brazil.
¹⁷ Department of Neurology, University of California Los Angeles and California Rehabilitation Institute, Los Angeles, CA, USA.
¹⁸ Department of Psychiatry and Clinical Psychobiology, University of Barcelona, Barcelona, Spain.
¹⁹ icometrix, Leuven, Belgium.
²⁰ Department of Computer Science, Technical University of Munich, Munich, Germany.
²¹ Functional Imaging Unit, Department of Diagnostic Radiology and Neuroradiology, University of Greifswald, Greifswald, Germany.
²² Departments of Neurology and Diagnostic Medicine, Dell Medical School at The University of Texas Austin, Austin, TX, USA.
²³ Department of Neurology, Duke University School of Medicine, Durham, NC, USA.
²⁴ Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA.
²⁵ Department of Psychiatry, NYU Grossman School of Medicine, New York, NY, USA.
²⁶ Department of Brain Sciences, Imperial College London, London, UK.
²⁷ Center for Data Science, Université Paris-Saclay, Inria, Palaiseau, France.
²⁸ Department of Health Sciences & Research, Medical University of South Carolina, Charleston, SC, USA.
²⁹ Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, USA.
³⁰ Innovation, Implementation and Clinical Translation (IIMPACT) in Health, Allied Health and Human Performance, University of South Australia, Adelaide, South Australia, Australia.
³¹ Ralph H Johnson VA Medical Center, Charleston, SC, USA.
³² The Florey Institute of Neuroscience and Mental Health, Heidelberg, VIC, Australia.
³³ Neuroradiology, School of Medicine, Technical University Munich, München, Germany.
³⁴ Department of Radiology, Tianjin Medical University General Hospital, Tianjin, China.
³⁵ Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
³⁶ Hurvitz Brain Sciences Program, Toronto, Ontario, Canada.
³⁷ Department of Clinical Psychology and Psychobiology, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain.
³⁸ Institut de Recerca Sant Joan de Déu, 08950, Esplugues de Llobregat, Spain.
³⁹ Jefferson Magnetic Resonance Imaging Center, Philadelphia, PA, USA.
⁴⁰ CatoSenteret Rehabilitation Center, SON, Norway.
⁴¹ Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway.
⁴² Inter-university Consortium for Political and Social Research, University of Michigan, Ann Arbor, MI, USA.
⁴³ Facility for Education and Research in Neuroscience, Emory University, Atlanta, GA, USA.
⁴⁴ ARTORG Center for Biomedical Engineering Research, University of Bern, Bern, Switzerland.
⁴⁵ Schlegel-University of Waterloo Research Institute for Aging, University of Waterloo, Waterloo, Ontario, Canada.
⁴⁶ Canadian Partnership for Stroke Recovery, Sunnybrook Research Institute, Toronto, Ontario, Canada.
⁴⁷ Department of Rehabilitation Sciences, Medical University of South Carolina, Charleston, SC, USA.
⁴⁸ Clinical Neurotechnology Laboratory, Dept. of Psychiatry and Neurosciences (CCM), Charité - Universitätsmedizin Berlin, Berlin, Germany.
⁴⁹ Menninger Department of Psychiatry and Behavioral Sciences, Division of Neuropsychiatry, Baylor College of Medicine, Houston, TX, USA.
⁵⁰ Department of Physical Therapy and Neuroscience, Samson College of Health Sciences, St. Joseph's University, Philadelphia, PA, USA.
⁵¹ Department of Psychology, University of Oslo, Oslo, Norway.
⁵² NORMENT, Department of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.
⁵³ Division of Biokinesiology and Physical Therapy of the Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA.
⁵⁴ Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
⁵⁵ Geriatrics Research, Education and Clinical Center, HERL, Department of Veterans Affairs, Pittsburgh, PA, USA.
⁵⁶ Departments of Neurology, PM&R, RNEL, CNBC, University of Pittsburgh, Pittsburgh, PA, USA.
⁵⁷ Department of Physical Medicine & Rehabilitation, Dell Medical School, University of Texas at Austin, Austin, TX, USA.
⁵⁸ Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China.

^# Contributed equally.

PMID: 35710678
PMCID: PMC9203460
DOI: 10.1038/s41597-022-01401-7

Abstract

Accurate lesion segmentation is critical in stroke rehabilitation research for the quantification of lesion burden and accurate image processing. Current automated lesion segmentation methods for T1-weighted (T1w) MRIs, commonly used in stroke research, lack accuracy and reliability. Manual segmentation remains the gold standard, but it is time-consuming, subjective, and requires neuroanatomical expertise. We previously released an open-source dataset of stroke T1w MRIs and manually-segmented lesion masks (ATLAS v1.2, N = 304) to encourage the development of better algorithms. However, many methods developed with ATLAS v1.2 report low accuracy, are not publicly accessible or are improperly validated, limiting their utility to the field. Here we present ATLAS v2.0 (N = 1271), a larger dataset of T1w MRIs and manually segmented lesion masks that includes training (n = 655), test (hidden masks, n = 300), and generalizability (hidden MRIs and masks, n = 316) datasets. Algorithm development using this larger sample should lead to more robust solutions; the hidden datasets allow for unbiased performance evaluation via segmentation challenges. We anticipate that ATLAS v2.0 will lead to improved algorithms, facilitating large-scale stroke research.

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Conflict of interest statement

A.G.B. serves on the Biogen Australia Dementia Scientific Advisory Committee and editorial boards of Neurology and International Journal of Stroke. S.C.C. serves as a consultant for Abbvie, Constant Therapeutics, MicroTransponder, Neurolutions, SanBio, Panaxium, NeuExcell, Elevian, Medtronic, and TRCare. E.d.L.R. is employed by icometrix. C.A.H. serves on the Advisory Board for Welcony Magstim and as a Consultant for Brainsway. B.G.H. has a clinical partnership with Fourier Intelligence. J.S.K. is cofounder of BoneScreen GmbH. G.F.W. serves on the Scientific Advisory Board for Myomo, Inc.

Figures

**Fig. 1**
Example of Lesion Segmentation in ITK-SNAP. An example of the ITK-SNAP interface displaying a lesion segmentation mask (red) in radiological convention (the left hemisphere is shown on the right side of the screen). Axial (top left), sagittal (top right), and coronal (bottom right) planes are shown. A video of the example lesion mask in ITK-SNAP can be viewed through Schol-AR by scanning the QR code in the bottom left with a mobile device, or by opening this PDF with a non-mobile web browser at www.Schol-AR.io/reader.

**Fig. 2**
Lesion Tracing and Preprocessing Pipeline. A flowchart diagram demonstrating the process for creating the two archived datasets: a raw dataset in native space archived with the Archive of Data on Disability to Enable Policy and research (ADDEP) (left blue box) and a preprocessed dataset in MNI-152 space archived with the International Neuroimaging Data-Sharing Initiative (INDI) (right blue box).

**Fig. 3**
Example of Visual Quality Control. Example of an image used to ensure proper registration of each subject’s brain (gray) and lesion segmentation mask (reddish brown) to the MNI template (green).

**Fig. 4**
Probabilistic Lesion Overlap Map on the MNI_icbm152 Template. Visualization of the lesion overlap across all subjects (N = 955) overlaid on the MNI template, with hotter colors representing more subjects with lesions at that voxel. An interactive volumetric 3D display of this data may be viewed through Schol-AR by scanning the QR code from Fig. 1 with a mobile device, or by opening this PDF with a non-mobile web browser at www.Schol-AR.io/reader.

See this image and copyright information in PMC

References

1. Liew S-L, et al. The ENIGMA Stroke Recovery Working Group: Big data neuroimaging to study brain-behavior relationships after stroke. Human brain mapping. 2022;43:129–148. doi: 10.1002/hbm.25015. - DOI - PMC - PubMed
1. Liew, S.-L. et al. Smaller spared subcortical nuclei are associated with worse post-stroke sensorimotor outcomes in 28 cohorts worldwide. Brain Communications, 10.1093/braincomms/fcab254 (2021). - PMC - PubMed
1. Boyd LA, et al. Biomarkers of stroke recovery: Consensus-based core recommendations from the Stroke Recovery and Rehabilitation Roundtable. Neurorehabilitation and neural repair. 2017;31:864–876. doi: 10.1177/1545968317732680. - DOI - PubMed
1. Feng W, et al. Corticospinal tract lesion load: An imaging biomarker for stroke motor outcomes. Ann Neurol. 2015;78:860–870. doi: 10.1002/ana.24510. - DOI - PMC - PubMed
1. Kim B, Winstein C. Can neurological biomarkers of brain impairment be used to predict poststroke motor recovery? A systematic review. Neurorehabilitation and neural repair. 2017;31:3–24. doi: 10.1177/1545968316662708. - DOI - PubMed

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A large, curated, open-source stroke neuroimaging dataset to improve lesion segmentation algorithms

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A large, curated, open-source stroke neuroimaging dataset to improve lesion segmentation algorithms

Authors

Affiliations

Abstract

Conflict of interest statement

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