ICA-FIX Multi Run - HCP Early Psychosis
Matthew Danyluik
Glasser, Matthew
Did you run all the HCP Pipelines on this data?
hp=2000 We recommend hp0.
doMotionRegression: TRUE We recommend false (see Glasser et al., 2019 Neuroimage supplemental for why). Perhaps there is a bug in motion regression as it is not tested any more as a mainline feature.
I’m not sure how you got down this road, so I have gone in and updated the sICA+FIX example Batch script comments to more clearly steer users to our recommended settings.
Matt.
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Matthew Danyluik
Glasser, Matthew
Did you process from the raw data?
hp=2000 and hp=0 are highly similar, it is just that hp=0 takes seconds to compute and hp=2000 takes a long time.
We have backed out movement regression from all HCP-YA data in our updated release (which also has temporal ICA cleanup).
As far as I know, HCD has not yet been released, but we will be hoping to do that in the future.
Matt.
From:
Matthew Danyluik <mattda...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Thursday, October 23, 2025 at 8:37 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Glasser, Matthew" <glas...@wustl.edu>
Subject: Re: [hcp-users] ICA-FIX Multi Run - HCP Early Psychosis
Hi Matt -
Thank you for your reply. As mentioned, data was previously processed with fMRIVolume and fMRISurface. Structural images were previously fully processed with HCP pipelines as well.
As for how I got down this road, I simply followed what was done for the FIX-processed data for HCP-1200, which included bp=2000 and 24-parameter motion regression. I'm working with the HCP 1200, Development, and Early Psychosis datasets, and want to keep processing as similar as possible between them.
If guidance has been updated since then (I see the 1200 data release document is dated April 2018, so before the article you reference), then an update to the docs is very welcome.
On Wednesday, October 22, 2025 at 9:05:53 PM UTC-4 glas...@wustl.edu wrote:
Did you run all the HCP Pipelines on this data?
hp=2000 à We recommend hp0.
doMotionRegression: TRUE à We recommend false (see Glasser et al., 2019 Neuroimage supplemental for why). Perhaps there is a bug in motion regression as it is not tested any more as a mainline feature.
I’m not sure how you got down this road, so I have gone in and updated the sICA+FIX example Batch script comments to more clearly steer users to our recommended settings.
Matt.
From: Matthew Danyluik <mattda...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, October 22, 2025 at 6:29 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] ICA-FIX Multi Run - HCP Early Psychosis
Hi there -
I'm using IcaFixProcessingBatch.sh to run the hcp_fix_multi_run pipeline on rs-fMRI data from the HCP Early Psychosis dataset, previously processed with fMRIVolume and fMRISurface. I'm running v5.0.0 of the HCP pipelines and pyfix as distributed with FSL 6.0.7.18. The pipeline succeeds for all but 5 subjects in the dataset, who fail with the error message:
ERROR: Movement_Regressors.txt not retrieved properly.
For each subject this error occurs for, Movement_Regressors.txt seems to exist and not be corrupted for each acquisition. I'm attaching an example .o log file here for reference.
Please let me know if you need any more details, and thank you in advance for your help.
Matthew.
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Matthew Danyluik
Harms, Michael
Or, if you want to cite from a publicly available resource as the source of your HCP-YA data, download from the latest release (HCP-Young Adult 2025):
https://balsa.wustl.edu/project?project=HCP_YA
cheers,
-MH
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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