By: Hailey D'Silva, Neuroimaging Data Analyst, Yale School of Medicine (https://doi.org/10.18116/c4rt-aj48)
Cloud computing allows you to borrow compute resources on a pay-as-you-go basis. Research groups who were previously limited to running their analyses on their local or institutional systems can now choose a cloud platform to flexibly and scalably borrow the compute resources they need. Neuroimaging datasets are getting larger, creating greater storage and compute demands, and many of the largest neuroimaging datasets are already hosted on cloud platforms. This has prompted some researchers to wonder how they can work with data in the cloud, but migrating workflows and building data pipelines from scratch on a cloud platform can present a significant challenge.
We are proud to present NeuroStack, built through a collaboration between researchers at the Yale School of Medicine and the University of Massachusetts Medical School. NeuroStack is a tool to aid researchers working with neuroimaging data using AWS cloud computing. Little to no AWS experience is needed to use NeuroStack, and it is freely available to the research community on the NITRC website. When you download NeuroStack, you build a pipeline of AWS resources optimized for neuroimaging workflows into your AWS account. Researchers who previously would have needed to spend hours learning about and building AWS services from scratch can now use NeuroStack to immediately begin working with their data. To use NeuroStack, simply modify and upload a template script to fit your needs and upload your data. Your uploaded data will immediately begin processing according to your script.
What types of workflows can you use NeuroStack for? NeuroStack contains the NITRC computational environment (NITRC-CE), which means you can use NeuroStack to work with any of the software available in the NITRC-CE. This includes FSL, SPM, AFNI, FreeSurfer, PLINK, 3D Slicer, MRIcron, DTIPrep, scikit-learn, NEURON, and more.
You can download NeuroStack and find detailed instructions here. Watch the NeuroStack introduction video here.
Quarterly Newsletter Article from March 15, 2022