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CPAC Connectome Analysis in the Cloud


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Harnessing cloud computing to achieve high-throughput connectomes analysis.

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CPAC Connectome Analysis in the Cloud

  1. 1. Harnessing cloud computing for high capacity analysis of neuroimaging data Cameron Craddock, PhD Computational Neuroimaging Lab Center for Biomedical Imaging and Neuromodulation Nathan S. Kline Institute for Psychiatric Research Center for the Developing Brain Child Mind Institute
  2. 2. Discovery science in Psychiatric Neuroimaging 1. Characterizing inter-individual variation in connectomes (Kelly et al. 2012) 2. Identifying biomarkers of disease state, severity, and prognosis (Craddock 2009) 3. Re-defining mental health in terms of neurophenotypes, e.g. RDOC (Castellanos 2013) Data is often shared only in its raw form – must be preprocessed to remove nuisance variation and to be made comparable across individuals and sites.
  3. 3. Connectomics is Big Data
  4. 4. Configurable Pipeline for the Analysis of Connectomes (CPAC) • Pipeline to automate preprocessing and analysis of large-scale datasets • Most cutting edge functional connectivity preprocessing and analysis algorithms • Configurable to enable “plurality” – evaluate different processing parameters and strategies • Automatically identifies and takes advantage of parallelism on multi-threaded, multi-core, and cluster architectures • “Warm restarts” – only re-compute what has changed • Open science – open source • Nypipe
  5. 5. Computing in the Amazon Cloud • No hardware capital cost • No hardware maintenance • No software installation or configuration* • Resources scale to meet need for no overhead • Available everywhere and to everybody • Allows access to exotic architectures, such as GPUs *If appropriate AMI is available
  6. 6. Amazon EC2 - Instance • The hardware on which your processing will run:
  7. 7. Instance Pricing • On-demand Pricing – Always available, fixed price, non-interruptible, most stable • Spot instances – Market to sell otherwise unused time, variable price, interruptible
  8. 8. Spot Instances • Prices fluctuate over time • If price exceeds the max you are willing to pay, your instances are terminated
  9. 9. Storage • S3 – Simple Storage Service – Secure and stable storage with a web service interface, pay for what you use – Big and slow, $0.03 per GB/Month – Can be accessed from anywhere • EBS – Elastic Block Storage – Provisioned storage (SSD HD) directly connected to instance, pay for what you provision – Fast and expensive, $0.10 per GB/Month – Persistent and transferrable • Instance Storage – SSD storage provided with some instances, included in instance price – Fast and free – Non-persistent and non-transferrable – good for cache
  10. 10. Amazon EC2 - Instance • The hardware on which your processing will run:
  11. 11. Data Transfer • In general, free in - pay out – Out to other Amazon service such as S3, EBS, etc is free – Out to Internet is $0.09 per GB (becomes slightly cheaper after 10TB or so)
  12. 12. Amazon Machine Images • Virtual machines that provide the software environment for your processing • You can build your own, or use one maintained by others
  13. 13. StarCluster • Star cluster simplifies the process of building a Sun Grid Engine based cluster in EC2 – Dynamically add and remove compute nodes – Uses spot instances – Provides scripts for performing many administrative tasks
  14. 14. C-PAC Amazon Machine Image Nypipe
  15. 15. Proof of concept • Preprocessed 1,112 datasets from ABIDE with C-PAC – 4 different preprocessing strategies (+/- temporal filter, +/- global signal regression) – 24 derivatives: • ReHo, ALFF, fALFF, 10 RSNs, VMHC, binary degree centrality, weighted degree centrality, lFCD, time courses for 5 atlases (AAL, TT, EZ, HO, CC200, CC400)
  16. 16. • Requires 45 minute to process 1 dataset • 3 datasets can be processed in parallel • Processing results in .5GB of data Model Parameters
  17. 17. Cloud vs. Traditional Computing 0 5000 10000 15000 100 2000 5000 10000 15000 20000 25000 30000 35000 40000 45000 50000 Number of Datasets Cost($) Instance Cost Storage Cost Transfer Cost 0 4000 8000 12000 100 2000 5000 10000 15000 20000 25000 30000 35000 40000 45000 50000 Number of Datasets Time(hours) No Download Total Processing Time
  18. 18. Impact of Spot Instances Simulations using past 90 days of spot price history
  19. 19. Other Pipelines
  20. 20. What about HIPAA? • Amazon AWS meets FedRAMP and NIST 800-53 standards, which are more rigorous than HIPAA – Access to instances controlled using 256-bit AES – Default firewalls deny all outside access – EC2, EBS, and S3 storage are compatible with encryption • AWS HIPAA whitepaper – PAA_Compliance_Whitepaper.pdf
  21. 21. C-PAC Amazon Machine Image Nypipe
  22. 22. Preprocessed INDI Data in the Cloud • Available through S3 Bucket generously provided by AWS • Raw INDI will be available soon
  23. 23. - HCP Data available in the cloud: - - Receive $100 AWS Credits at the HCP workshop in Hawaii - connectome.php
  24. 24. Acknowledgements CPAC Team: Daniel Clark, Steven Giavasis and Michael Milham. NDAR “Cloud Team”: Christian Haselgrove, Dave Kennedy, and Jack van Horn. NDAR Team: Dan Hall, Brian Koser, David Obenshain, Svetlana Novikova, and Malcom Jackson. CPAC-NDAR integration was funded by a contract from NDAR. ABIDE Preprocessed data is hosted in a Public S3 Bucket provided by AWS.