Hello NeuroStart community, hope you are all doing fine.
I have decided to use FMRIPREP to preprocess 240 subjects from ADNI website, each of my subjects has one fMRI scan and one MRI scan, I have decided to rent a HPC to do the preprocessing step, but I don’t exactly know how much ram and CPU and storage do I need to do this, my initial plan was to get 120 cores of CPU, 256 GB of ram and 2TB of storage and rent that HPC for 5 days, could you please kindly clarify that it would be enough or do I need to rent it for longer duration?
Hi @Alireza217,
Looks like you could run 15 subjects with 8 CPUs and 16 GB concurrently. Estimating about 12 hours per subject, 5 days would be able to process 150 subjects.
To get through 240 subjects in 5 days you would need to process 48 subejcts per day, or 24 subjects concurrently assuming 12 hour run time. That would limit you to 4 cores and 10GB per subject. That might be possible, but could also be slower per subject and not enough memory.
You can try running on brainlife.io for free cloud based HPC processing.
2TB should be fine.
Best,
Steven
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Thank you so much! I appreciate your help, since I’m new to the field and this is my first project, I did not know anything about brainlife.io, could you please tell me that if this website offers free hardware resources to use tasks like FMRIPREP preprocessing? honestly I did not understand that from their website.
Hi @Alireza217,
Yes brainlife.io allows you to access HPC resources and run apps (such as fmriprep) from the cloud. You must upload your data to their portal first.
Best,
Steven
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