Introduction to NeuroStack for Cloud-Based Neuroimaging Processing

Explore the capabilities of NeuroStack, a cloud-based platform for neuroimaging processing on AWS. Learn how to convert file types, process subjects in FreeSurfer, and leverage AWS for scalable computing. Discover the steps to install NeuroStack, its functionalities, and the services it offers for efficient data processing in the field of neuroscience.

• NeuroStack
• Cloud Computing
• Neuroimaging
• AWS Services
• Data Processing

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Uploaded on Aug 13, 2024 | 0 Views

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1. NeuroStack DEMO Presenter: Hailey D Silva

2. Agenda 02 03 01 NeuroStack (AFNI) A simple example of converting file types NeuroStack (FreeSurfer) Processing a subject in FreeSurfer AWS Basics A primer on AWS

3. 01 AWS Basics A Primer on AWS

4. AWS is a cloud computing platform Scalable, no need to buy and maintain local infrastructure What is AWS? Large research datasets are increasingly being hosted on cloud platforms, especially AWS

5. Relevant Services EC2 Compute Lambda IAM Event-driven computing Access Management S3 Storage Batch CloudFormation Batch computing Infrastructure automation

6. Install NeuroStack 1. Log into your AWS account 2. Click 3. Continue choosing Next 4. Accept that IAM permissions will be created 5. Create Stack

7. How does NeuroStack work?

8. 02 - NeuroStack (AFNI) A simple example of converting file types 1. Add neurostack_script.sh to the neurostack-script S3 bucket 2. Add test.nii to the neurostack-input S3 bucket 3. (Optional) Watch your job process through Batch 4. After several minutes, your processed data will be automatically uploaded to the neurostack-output S3 bucket

9. NITRC-CE Software FSL SPM AFNI FreeSurfer PLINK 3D Slicer MRIcron Connectome Viewer DIPY Diffusion Imaging Analysis BrainSuite DTIPrep Scikit-learn C-PAC MaCH NEURON Mrtrix NIPY File IO NIPY Structural and Functional NIPY Pipeline and Interfaces DWI/DTI Quality Control Tool Solar Eclipse Imaging Genetics Tools

10. 03 - NeuroStack (FreeSurfer) Using NeuroStackto process a subject in FreeSurfer 1. Add neurostack_script.sh (from the freesurfer folder) to the neurostack-script S3 bucket 2. Add license.txt to the neurostack-script S3 bucket 3. Add test.nii to the neurostack-input S3 bucket 4. (Optional) Watch your job process through Batch 5. After a few hours, your processed data will be automatically uploaded to the neurostack-output S3 bucket

11. Clean Up Once everything is done 1. Delete everything in your NeuroStack S3 buckets 2. Delete NeuroStack from your CloudFormation stacks

12. THANKS Funding From: Funding From: The Amazon Web Services (AWS) Promotional Credit Program The Manton Foundation The Eunice Kennedy Shriver National Institute of Child Health and Human Development (P50HD027802) Project Authors: Project Authors: Hailey D Silva Christian Haselgrove Joan Bosson-Heenan, MPH Jeffrey Gruen, MD Presentation Credits: Presentation Credits: Presentation template by Slidesgo Icons by Flaticon Infographics by Freepik A Special Thank You to the Gruen Laboratory