combining data processed with different versions of the HCP Pipelines
Ely, Benjamin A.
Hi everyone,
I’ve been processing data using an early version of the HCP Pipelines (v3.27), including ICA-FIX through MSMAll steps. However, recent updates to the computer cluster I use mean that FreeSurfer 5.3.0-HCP no longer runs in that environment, and I also am not able to do a local installation due to the age of the installer. The straightforward thing to do is move to a current version of the pipelines (ideally a containerized version to avoid this issue in the future), but I’m concerned about compatibility between data processed with older vs. current versions. Reprocessing the existing data isn’t feasible due to the number of participants (>200) and the time already invested in QC/resolving issues/etc.
Is there a recommended approach for this, and are there any known issues with combining data processed with different HCP Pipeline versions?
Thanks so much,
-Ely
Benjamin A. Ely, PhD
Assistant Professor
Department of Psychiatry & Behavioral Sciences
University of Miami Miller School of Medicine
Harms, Michael
Not really -- the "recommended approach" is not to mix versions.
Some of the specific sub-pipelines may be more impacted than others, and certain downstream measures may be more impacted than others. There is no simple answer to your question.
Cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
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Harms, Michael
I don't recall exactly when we started releasing containerized versions of the HCPpipelines in QuNex.
There *might* be an old QuNex container that is based on that old version of the HCPpipelines, or at least gets you substantially closer.
Cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
Elam, Jennifer
We announced the first public release of QuNex v0.90.6 in May 2021 and it had HCP-pipelines v4.3.0 in it. Likely there’s a way to download that previous version from QuNex either from the site or by contacting them directly (CC’d).
Best,
Jenn
________________________________________
Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/E08F6C27-FC43-4CCC-BD58-9E8BFFC8CC2D%40wustl.edu.
Harms, Michael
In that case, you're probably not going to find a QuNex container that takes you all the way back to HCPpipelines v3.27, which was released back in June 2018.
You might be able to find a container somewhere that runs FreeSurfer 5.3.0-HCP, and then try to run HCPpipelines v3.27 inside that container?
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
Ely, Benjamin A.
Thanks so much for your prompt feedback. Will ponder the options with my team. Will likely try running some already-processed subjects through the initial QuNex release and compare the outputs, since that’s the closest readily available version.
Appreciatively,
-Ely
Benjamin A. Ely, PhD
Assistant Professor
Department of Psychiatry & Behavioral Sciences
University of Miami Miller School of Medicine
From:
Ely, Benjamin A. <ba...@med.miami.edu>
Date: Tuesday, November 18, 2025 at 3:40
PM