Not sure if there's a quick fix within SPM, but what we've done when we ran into that issue is wrap our preprocessing steps within another function that first copies the subject's data to a scratch directory on a local hard drive on the system doing the processing, then it does the required processing, and then it copies the processed data back to the network location. This provides a great deal of speed up on our NAS for some of those steps that produce large numbers of small I/O operations.
-Mike
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Mike Angstadt
Research Computer Specialist / PANLab Lab Manager
Department of Psychiatry / University of Michigan
(734) 936-8229
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of West, John D.
Sent: Tuesday, September 27, 2016 12:56 PM
To: [log in to unmask]
Subject: [SPM] Tweaking SPM I/O
Hello.
I wanted to get folks take on if it is possible to tweak SPM's I/O patterns. We've recently moved to a new storage system that while secure and has good I/O for large files, small intermittent I/O suffers. For example, Slice Timing Correction has I/O that writes one slice at a time to each fMRI volume. Which for 300 volumes at 50 slices each corresponds to 15000 small writes. Is there any way to tweak SPM's I/O to write all volumes at once or a volume at a time? I'm sure there are ways to modify the code to allow this, but I wasn't sure if there was a quick fix (option) or if this I/O pattern is important to how SPM functions and does its processing.
Any insight would be most appreciated.
Thanks.
John D. West, M.S.
Systems Administrator | Center for Neuroimaging
Indiana University School of Medicine
355 West 16th Street | GH 4100
Indianapolis, IN 46202
317-963-7510
mailto:[log in to unmask]
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