towards open and reproducible neuroscience in the age of big data

Towards open and reproducible neuroscience in the age of big data

Chris GorgolewskiCenter for Reproducible NeuroscienceStanford University

ON THE IMPORTANCE OF DATA

ROSALIND FRANKLIN AND PHOTOGRAPH 51

NEUROVAULT.ORG DATA REUSE

Sochat et al. 2015

OPENFMRI DATA REUSE

Gorgolewski et. al 2015

DATA SHARING SAVES MONEY

$878,988COST OF REACQUIRING DATA FOR EACH OF THE REUSES OF

OPENFMRI DATASETS (2015)

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: 10.1371/journal.pone.0026828

SHARING DATA IS RELATED TO HIGHER CITATION RATE

PIWOWAR, DAY & FRIDSMA (2007)

Piwowar & Vision(2013)

MAKING MORE DATA ACCESSIBLE TO

MORE RESEARCHERS

MEET PROF. SMITH

BIDS.NEUROIMAGING.IO

MEET MIKE


GETTING LOST IN YOUR DATA



HETEROGENEITY IN DATA DESCRIPTION PRACTICES CAUSES:• PROBLEMS IN SHARING DATA,• UNNECESSARY MANUAL METADATA

INPUT,• NO WAY TO AUTOMATICALLY VALIDATE

DATASETS.



• MRI HAS BEEN USED TO STUDY THE HUMAN BRAIN FOR OVER 20 YEARS.

• DESPITE SIMILARITIES IN EXPERIMENTAL DESIGNS AND DATA TYPES EACH RESEARCHER TENDS TO ORGANIZE AND DESCRIBE THEIR DATA IN THEIR OWN WAY.

http://www.nature.com/news/brain-imaging-fmri-2-0-1.10365


BRAIN IMAGING DATA STRUCTURE

A NEW STANDARD FOR ORGANIZING HUMAN

NEUROIMAGING DATASETS


WHO IS IT FOR?

1.LAB PIS. IT WILL MAKE HANDING OVER ONE DATASET FROM ONE STUDENT/POSTDOC TO ANOTHER EASY.

2.WORKFLOW DEVELOPERS. IT’S EASIER TO WRITE PIPELINES EXPECTING A PARTICULAR FILE ORGANIZATION.

3.DATABASE CURATORS. ACCEPTING ONE DATASET FORMAT WILL MAKE CURATION EASIER.


WHO IS IT FOR?


PRINCIPLES BEHIND BIDS

1.ADOPTION IS CRUCIAL. 2.DON’T REINVENT THE

WHEEL. 3.80/20 RULE.


EVOLUTION OF BIDS1.KICKOFF MEETING AT STANFORD IN

SPRING 20152.MEETING AT OHBM 2015 (JUNE)3.INTRODUCED TO NEUROINFORMATICS

COMMUNITY AT NEUROINFORMATICS CONGRESS 2015 (AUGUST)

4.FIRST RELEASE CANDIDATE AND PUBLIC CALL FOR COMMENTS (SEPTEMBER)

5.VERSION 1.0.0 PUBLISHED ALONG A INTRODUCTORY PAPERBIDS.NEUROIMAGING.I

O

COMMUNITY OUTREACH

• REACHED OVER 5000 RESEARCHERS• EXCHANGED HUNDREDS OF EMAIL

COMMENTS PRODUCED • ~40 EXAMPLE DATASETS

• 27 COAUTHORS ON THE FINAL MANUSCRIPT


Gorgolewski et al. (2016) Scientific Data

FOLDER ORGANIZATION


FOLDER ORGANIZATION

participant_id age sex sub-001 34 M sub-002 12 F sub-003 33 F


FOLDER ORGANIZATION

NIfTI


FOLDER ORGANIZATION

{ "RepetitionTime": 3.0, "EchoTime": 0.03, "FlipAngle": 78, "SliceTiming": [0.0, 0.2, 0.4, …], "MultibandAccellerationFactor": 4, "PhaseEncodingDirection": "j-" }


THE VALIDATOR

incf.github.io/bids-validator/


http://incf.github.io/bids-validator/

PROF. SMITH(2030)


SOFTWARE SUPPORTING BIDS

• QAP (QUALITY ASSESMENT)• MRIQC (QUALITY ASSESMENT)• FMRIPREP (PREPROCESSING WORKFLOW)• AUTOMATIC ANALYSIS (FMRI PROCESSING TOOLBOX)• OPENFMRI2BIDS (CONVERTER)• BIDS2ISATAB (CONVERTER)• DCM2NIIX (CONVERTER)• DICM2NII (CONVERTER)• OPENFMRI (REPOSITORY)• BIDSTO3COL (CONVERTER)• BIDS2NDA (CONVERTER)• AFNI BIDS-TOOLS (SET OF TOOLS FOR CONVERTING TO AND ANALYZING BIDS DATASETS IN

AFNI)• HEUDICONV (CONVERTER)• DCM2BIDS (CONVERTER)• C-PAC (CONFIGURABLE PIPELINE FOR THE ANALYSING CONNECTOMES)• BRAINSTORM (MEG/EEG ANALYSIS PACKAGE)

http://preprocessed-connectomes-project.org/quality-assessment-protocol/

http://mriqc.readthedocs.org/

https://github.com/poldracklab/preprocessing-workflow

https://github.com/rhodricusack/automaticanalysis

https://github.com/INCF/openfmri2bids

https://github.com/INCF/BIDS2ISATab

https://github.com/neurolabusc/dcm2niix

https://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter--nifti-tool-and-viewer

http://openfmri.org/

https://github.com/INCF/bidsutils/tree/master/BIDSto3col

https://github.com/INCF/BIDS2NDA

https://github.com/nih-fmrif/BIDS-tools

https://github.com/nipy/heudiconv

https://github.com/cbedetti/Dcm2Bids

http://fcp-indi.github.io/

http://neuroimage.usc.edu/brainstorm/

BIDS APPS

BIDS-APPS.NEUROIMAGING.IO

PORTABLE NEUROIMAGING PIPELINES THAT SUPPORT

BIDS DATASETS

BIDS APPS


BIDS APPS - CONTAINERS


• BATTERIES INCLUDED – NO NEED TO INSTALL ANY EXTRA SOFTWARE

• NO NEED TO WORRY ABOUT INCOMPATIBLE THIRD PARTY SOFTWARE UPDATES

• EASY TO SWITCH BETWEEN VERSIONS• WORKS ON WINDOWS, MAX, LINUX AND MULTI USER HPC

WHAT IS DOCKER?

• DOCKER IS THE MOST POPULAR CONTAINER IMPLEMENTATION• IT CONSISTS OF:• DOCKER ENGINE (RUNS CONTAINERS)• DOCKER HUB (CENTRALIZED WEB SERVICE

FOR STORING AND SHARING CONTAINER IMAGES)


RUNNING CONTAINERS ON CLUSTERS/HPCS

• DOCKER HAS LIMITATIONS:• IT WAS DESIGNED FOR THE CLOUD,

WHERE YOU ARE IN TOTAL CONTROL• REQUIRES MODERN KERNEL VERSION• ALLOWS USERS TO GAIN ROOT ACCESS



• THE ADVANCED DOCKER FEATURES ARE USEFUL FOR:• NETWORKING MANAGEMENT• SANDBOXING RESOURCES• MAPPING USERNAMES

• ALL SCIENTISTS CARE ABOUT IS PORTABILITY (CAPTURING BINARY DEPENDENCIES)


• SINGULARITY IS A CONTAINER FRAMEWORK THAT• WAS BUILD GROUND UP TO SUPPORT

CLUSTERS/HPCS• HAS MINIMAL REQUIREMENTS• RUNS ON LEGACY KERNELS• DOES NOT ELEVATE PERMISSIONS• ALLOWS IMPORTING DOCKER IMAGES


BIDS APPS - PARALLELIZATION


BIDS APPS - COMMUNITY

BIDS-APPS.NEUROIMAGING.IO GORGOLEWSKI ET. AL 2017

22 AVAILABL

E BIDS APPS


BIDS APPS - VERSIONING


EXAMPLE BIDS APPS: MRIQC AND FMRIPREP

MRIQC – QUALITY CONTROLFOR STRUCTURAL AND FUNCTIONAL IMAGES

MRIQC.ORG

SPIKES

CROWDSOURCING ARTEFACTS

WHAT HAPPENS WHEN YOU ASK TWITTER FOR HELP...

FMRIPREPROBUST EASY TRANSPARENT

FMRIPREP.READTHEDOCS.IO

WHAT IS IT?FMRI DATA PREPROCESSING

TOOL

PREPROCESSING?DENOISING AND NORMALIZATION


WHAT IT IS NOT

GLMDCM

CONNECTIVITYDYNAMICS

ETC.FMRIPREP.READTHEDOCS.I

O

FMRIPREP: PRINCIPLES

• EASY TO INSTALL AND USE

• ROBUST – WORKS ON ANY* DATA

• TRANSPARENT – “GLASS BOX” RATHER THAN “BLACK BOX”


FMRIPREP: T1W PREPROCESSING

• N4 BIAS FIELD CORRECTION (ANTS)

• SKULL STRIPPING (ANTS)

• 3 CLASS TISSUE SEGMENTATION (FSL FAST)

• ROBUST MNI COREGISTRATION (ANTS)FMRIPREP.READTHEDOCS.I

O

FMRIPREP: EPI PREPROCESSING

• MOTION CORRECTION (FSL MCFLIRT)

• SKULL STRIPPING (NILEARN)

• COREGISTRATION TO T1(FSL FLIRT WITH BBR)


REPORTS

BIDS DERIVATIVES

MAKING MORE DATA ACCESSIBLE TO MORE RESEARCHERS

Poldrack and Gorgolewski, 2014

MAKING MORE DATA ACCESSIBLE TO

MORE RESEARCHERS

OPENNEURO*

*BORN OUT OF A TWEET

FEATURES

• DATA ORGANIZATION – BIDS• DATA MANAGEMENT PLATFORM• UPLOADING• VALIDATION• SNAPSHOTING• DOWNLOADING

• DATA ANALYSIS – BIDS APPS

UPLOADING

BROWSING AND VALIDATION

ANALYSIS RESULTS

FUTURE DIRECTIONS

• HYPOTHESIS GENERATION MACHINE• SAME MODEL, SAME DATA, NEW BRAIN-BEHAVIOR

RELATIONSHIPS• VIBRATION RATIO ESTIMATION

• HOW MUCH YOUR RESULTS DEPEND ON PREPROCESSING DECISIONS (CARP 2012)

• EXPOSING NEUROIMAGING DATASETS TO ML COMMUNITY• FROM NIFTIS TO CSV FILES

• BIDS EXTENSIONS:• PET, MEG, MODELS, DERIVATIVES

ACKNOWLEDGMENTS

The Poldrack Lab @ StanfordData Sharing Task Force

ACKNOWLEDGMENTS

• TIBOR AUER • VINCE D. CALHOUN• R. CAMERON CRADDOCK• SAMIR DAS • EUGENE P. DUFF • GUILLAUME FLANDIN• SATRAJIT S. GHOSH • TRISTAN GLATARD • YAROSLAV O. HALCHENKO• DANIEL A. HANDWERKER• MICHAEL HANKE• DAVID KEATOR• XIANGRUI LI• DAN MARCUS

• ZACHARY MICHAEL• CAMILLE MAUMET• B. NOLAN NICHOLS• THOMAS E. NICHOLS• JOHN PELLMAN• JEAN-BAPTISTE POLINE• ARIEL ROKEM• CHRIS RORDEN• GUNNAR SCHAEFER• VANESSA SOCHAT• WILLIAM TRIPLETT• JESSICA A. TURNER • GAËL VAROQUAUX• RUSSELL A. POLDRACK

ACKNOWLEDGMENTS

• FIDEL ALFARO-ALMAGRO• PIERRE BELLEC • MIHAI CAPOTĂ • M. MALLAR CHAKRAVARTY• NATHAN W. CHURCHILL• ALEXANDER LI COHEN • GABRIEL A. DEVENYI• ANDERS EKLUND • OSCAR ESTEBAN• J. SWAROOP GUNTUPALLI• MARK JENKINSON• ANISHA KESHAVAN• GREGORY KIAR• FRANZISKUS LIEM

• PRADEEP REDDY RAAMANA• DAVID RAFFELT• CHRISTOPHER J. STEELE• PIERRE-OLIVIER QUIRION• ROBERT E. SMITH• STEPHEN C. STROTHER• GAËL VAROQUAUX• TAL YARKONI• YIDA WANG • ROSS BLAIR• SHOSHANA BERLEANT• SUYASH BHOGOWAR• JOSEPH WEXLER• CHRIS MARKIEWICZ

OHBM REPLICATION AWARD

BEST REPLICATION IN NEUROIMAGINGPEER REVIEWED PAPER OR PREPRINTPUBLISHED/POSTED ANYTIME BEFORE FEBRUARY 2017SUBMISSION DEADLINE: FEBRUARY 22 2017THE AWARD ($2000) WILL BE PRESENTED AT A PLENARY

SESSION OF OHBM 2017HTTP://WWW.HUMANBRAINMAPPING.ORG/I4A/PAGES/INDEX.C

FM?PAGEID=3731HTTP://WWW.OHBMBRAINMAPPINGBLOG.COM/BLOG/OHBM-R

EPLICATION-AWARD-QA-WITH-CHRIS-GORGOLEWSKI

http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3731

http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3731

http://www.ohbmbrainmappingblog.com/blog/ohbm-replication-award-qa-with-chris-gorgolewski

http://www.ohbmbrainmappingblog.com/blog/ohbm-replication-award-qa-with-chris-gorgolewski

HOW TO GET INVOLVED (WE NEED YOUR HELP!)

• SHARE YOUR DATA!• OPENFMRI.ORG (RAW) • NEUROVAULT.ORG (STATISTICAL MAPS)

• LEARN MORE ABOUT BIDS AND JOIN THE WORK ITS EXTENSIONS: • BIDS.NEUROIMAGING.IO

• CHECK OUT BIDS APPS, DEVELOP YOUR OWN: • BIDS-APPS.NEUROIMAGING.IO

• TRY MRIQC, LET US KNOW HOW TO MAKE IT BETTER: • MRIQC.ORG

• TRY FMRIPREP AND TELL US HOW IT WORKS WITH YOUR DATA: • FMRIPREP.READTHEDOCS.ORG

• APPLY FOR THE OHBM REPLICATION AWARD

towards open and reproducible neuroscience in the age of big data

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