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Towards open and reproducible neuroscience in the age of big data

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NIH and MIT - January 2017

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Towards open and reproducible neuroscience in the age of big data

  1. 1. Towards open and reproducible neuroscience in the age of big data Chris Gorgolewski Center for Reproducible Neuroscience Stanford University
  2. 2. Sochat et al. 2015
  3. 3. OPENFMRI DATA REUSE Gorgolewski et. al 2015
  4. 4. STUDIES SHARING DATA HAVE HIGHER STATISTICAL QUALITY Wicherts JM, Bakker M, Molenaar D (2011) Willingness to Share Research Data Is Related to the Strength of the Evidence and the Quality of Reporting of Statistical Results. PLoS ONE 6(11): e26828. doi:
  5. 5. SHARING DATA IS RELATED TO HIGHER CITATION RATE PIWOWAR, DAY & FRIDSMA (2007) Piwowar & Vision(2013)
  6. 6. MEET PROF. SMITH BIDS.NEUROIMAGING.I O
  7. 7. MEET MIKE BIDS.NEUROIMAGING.I O
  8. 8. GETTING LOST IN YOUR DATA BIDS.NEUROIMAGING.I O
  9. 9. • • • BIDS.NEUROIMAGING.I O
  10. 10. • • http://www.nature.com/news/brain-imaging-fmri-2-0-1.10365 BIDS.NEUROIMAGING.I O
  11. 11. BIDS.NEUROIMAGING.I O
  12. 12. 1. 2. 3. BIDS.NEUROIMAGING.I O
  13. 13. BIDS.NEUROIMAGING.I O
  14. 14. 1. 2. 3. BIDS.NEUROIMAGING.I O
  15. 15. 1. 2. 3. 4. 5. BIDS.NEUROIMAGING.I O
  16. 16. • • • • BIDS.NEUROIMAGING.I O Gorgolewski et al. (2016) Scientific Data
  17. 17. BIDS.NEUROIMAGING.I O
  18. 18. BIDS.NEUROIMAGING.I O
  19. 19. participant_id age sex sub-001 34 M sub-002 12 F sub-003 33 F BIDS.NEUROIMAGING.I O
  20. 20. NIfT I BIDS.NEUROIMAGING.I O
  21. 21. { "RepetitionTime": 3.0, "EchoTime": 0.03, "FlipAngle": 78, "SliceTiming": [0.0, 0.2, 0.4, …], "MultibandAccellerationFactor": 4, "PhaseEncodingDirection": "j-" } BIDS.NEUROIMAGING.I O
  22. 22. incf.github.io/bids-validator/ BIDS.NEUROIMAGING.I O
  23. 23. PROF. SMITH(2030) BIDS.NEUROIMAGING.I O
  24. 24. • QAP • MRIQC • FMRIPREP • AUTOMATIC ANALYSIS • OPENFMRI2BIDS • BIDS2ISATAB • DCM2NIIX • DICM2NII • OPENFMRI • BIDSTO3COL • BIDS2NDA • AFNI BIDS-TOOLS • HEUDICONV • DCM2BIDS • C-PAC • BRAINSTORM
  25. 25. BIDS- APPS.NEUROIMAGING.IO
  26. 26. BIDS- APPS.NEUROIMAGING.IO
  27. 27. BIDS- APPS.NEUROIMAGING.IO • • • •
  28. 28. BIDS- APPS.NEUROIMAGING.IO
  29. 29. • • • • BIDS- APPS.NEUROIMAGING.IO
  30. 30. • • • • BIDS- APPS.NEUROIMAGING.IO
  31. 31. • • • • •
  32. 32. • • • • • • BIDS- APPS.NEUROIMAGING.IO
  33. 33. BIDS- APPS.NEUROIMAGING.IO
  34. 34. BIDS- APPS.NEUROIMAGING.IO GORGOLEWSKI ET. AL 2017
  35. 35. BIDS- APPS.NEUROIMAGING.IO
  36. 36. BIDS- APPS.NEUROIMAGING.IO
  37. 37. MRIQC.ORG
  38. 38. FMRIPREP.READTHEDOCS.I O
  39. 39. FMRIPREP.READTHEDOCS.I O
  40. 40. FMRIPREP.READTHEDOCS.I O
  41. 41. • • • FMRIPREP.READTHEDOCS.I O
  42. 42. • • • • FMRIPREP.READTHEDOCS.I O
  43. 43. • • • FMRIPREP.READTHEDOCS.I O
  44. 44. BIDS DERIVATIVES
  45. 45. MAKING MORE DATA ACCESSIBLE TO MORE RESEARCHERS Poldrack and Gorgolewski, 2014
  46. 46. • • • • • • •
  47. 47. • • • • • • • •
  48. 48. ACKNOWLEDGMENTS The Poldrack Lab @ Stanford Data Sharing Task Force
  49. 49. ACKNOWLEDGMENTS • • • • • • • • • • • • • • • • • • • • • • • • • • • •
  50. 50. ACKNOWLEDGMENTS • • • • • • • • • • • • • • • • • • • • • • • • • • • •
  51. 51.       HTTP://WWW.HUMANBRAINMAPPING.ORG/I4A/PAGES/INDEX.CFM?PAGEID=3 731  HTTP://WWW.OHBMBRAINMAPPINGBLOG.COM/BLOG/OHBM-REPLICATION- AWARD-QA-WITH-CHRIS-GORGOLEWSKI
  52. 52. • • • • • • • • • • • •

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