Quality control procedures after pre-processing
Yang Hu
Reid, Erin
Sent: Monday, February 10, 2025 6:31 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] Quality control procedures after pre-processing
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Harms, Michael
Hi,
If you haven’t already, load the actual scene files in the StructuralQC and fMRIQC folders. The scene descriptions contain a lot of helpful information about what each scene (and thus each png snapshot) contains.
Absolute and Relative RMS use the FSL output from ‘mcflirt’ to define the summary movement measures. There used to be a relevant FSL technical document online, which you might be able to find on the FSL Wiki, or by searching the FSL archives. IIRC, the RelativeRMS values from ‘mcflirt’ are approximately one-half of Power’s FD definition of relative movement.
‘eddy’ has its own separate definition of absolute and relative movement. I don’t believe they are the same as ‘mcflirt’s.
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
From:
"'Reid, Erin' via HCP-Users" <hcp-...@humanconnectome.org>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Monday, February 10, 2025 at 4:29 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: Re: [hcp-users] Quality control procedures after pre-processing
Glasser, Matthew
We run some additional pipelines in HCP Lifespan to better clean the fMRI (improved spatial ICA classification and temporal ICA cleanup). Perhaps one day those data will be available for download somewhere (and for HCP-YA too).
Matt.
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Yang Hu
Thank you for your help. To confirm my understanding, if I plan to use the pre-processed HCP dataset released by the HCP CCF, it is not necessary to check the pre-processing results. However, if I decide to re-run the pre-processing of raw HCP data (e.g., because the pre-processed one has not yet been released), would I still need to ensure the quality after pre-processing? I believe that visually checking the snapshots would be enough, because the raw data quality was already examined before release and HCP Pipelines should be generally robust.
Sincerely,
Yang Hu
Harms, Michael
Just so there is no confusion, Erin was writing specifically about the structural QC.
The quality of the fMRI and dMRI data in the HCP processed data will vary across individuals and some level of review is appropriate and warranted.
--
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
From:
Yang Hu <huyan...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Monday, February 10, 2025 at 10:05 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Reid, Erin" <er...@wustl.edu>
Subject: Re: [hcp-users] Quality control procedures after pre-processing
Dear Erin,
Thank you for your help. To confirm my understanding, if I plan to use the pre-processed HCP dataset released by the HCP CCF, it is not necessary to check the pre-processing results. However, if I decide to re-run the pre-processing of raw HCP data (e.g., because
the pre-processed one has not yet been released), would I still need to ensure the quality after pre-processing? I believe that visually checking the snapshots would be enough, because the raw data quality was already examined before release and HCP Pipelines
should be generally robust.
Sincerely,
Yang Hu
在2025年2月11日星期二 UTC+8 06:27:41<er...@wustl.edu> 写道：
Hello Yang Hu,
Regarding #1, all T1w & T2w scans were visually examined before they were sent through the pipelines. If quality was subpar, a recollection was requested.
Regarding #3, all FreeSurfer results were visually examined as well. Some of them just by viewing the png files in the individual's MNINonLinear/StructuralQC/snapshots folder. However, most of the data was examined using the [subject].structuralQC.wb_scene in Workbench (wb_view) in order to rotate and view the entire surface as well as scroll through every slice of the MRI displaying the white and pial surface outlines.
There should be no need for anyone to do another round of quality control on the data, but if you do find something notable, we would appreciate the heads up.
Hopefully one of my colleagues will be able to help you with your other questions regarding DWI and REST processing.
Sincerely,
Erin Reid (she/her) | Sr Research Technician
Department of Neuroscience
Yang Hu
Dear Michael,
Based on the scene file, I was able to figure out the purpose of each PNG figure. I am still learning the Workbench and the HCP framework, which poses a significant challenge for me.
After doing some research, I believe that the RelativeRMS metric corresponds to Jenkinson's FD as cited in some papers. According to FSL's fsl_motion_outliers documentation (https://fsl.fmrib.ox.ac.uk/fsl/docs/#/registration/motion_outliers), RelativeRMS should be equivalent to the --fdrms option. The difference between RelativeRMS and AbsoluteRMS lies in the reference volume used: for RelativeRMS, the reference is the previous volume, while for AbsoluteRMS, the reference may be the first volume or the motion correction reference volume (e.g., the SBRef image). For quality control of head motion, RelativeRMS should be used. If my understanding is incorrect, please let me know.
Thank you for the reminder about the structural QC.
Sincerely,
Yang Hu
Yang Hu
Dear Matt,
Thank you for the information. I would like to stay updated with these advancements after I complete the basic workflow. As I am new to the HCP Pipelines, I have read the Glasser et al. (2013) and Glasser et al. (2018) papers (though many details require more time to fully digest). Are there any other key methodological papers specific to the HCP Pipelines that I should read (besides those related to FreeSurfer/FSL tools)? Is there an official list of reference papers that you would recommend?
References:
Glasser,
M. F., Sotiropoulos, S. N., Wilson, J. A., Coalson, T. S., Fischl, B.,
Andersson, J. L., ... & Wu-Minn HCP Consortium. (2013). The minimal
preprocessing pipelines for the Human Connectome Project. Neuroimage, 80, 105-124.
Glasser, M. F., Coalson, T. S., Bijsterbosch, J. D., Harrison, S. J., Harms, M. P., Anticevic, A., ... & Smith, S. M. (2018). Using temporal ICA to selectively remove global noise while preserving global signal in functional MRI data. Neuroimage, 181, 692-717.
Sincerely,
Yang Hu
Glasser, Matthew
Other worthwhile papers to read include Glasser et al., 2016 Nature, Glasser et al., 2016 Nature Neuroscience, Coalson et al., 2018 PNAS, Glasser et al., 2019 Neuroimage, and Glasser et al., 2022 Neuroimage.
Matt.
From: Yang Hu <huyan...@gmail.com>
Date: Monday, February 10, 2025 at 11:20 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Department of Neuroscience