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Subjects collected during these periods of temporal instability are flagged with the issue code C for the QC_Issue measure and a list of these subjects is also available on the QC Issues wiki.

Main HCP List of Issue C Subjects:

 


Issue code D: REST Scans with Prominent Artifact in rfMRI MPP data, but fixed by FIX

An evaluation of grayplots (Power 2016, ref below) and/or network matrices generated from each subject's minimally preprocessed rfMRI scan data revealed subjects across the entire HCP study with at least one REST scan (run) that showed prominent artifacts due either to coil problems (the majority of cases), or excessive subject motion. A spreadsheet listing the REST scans exhibiting these artifacts is available on the QC Issues wiki. We believe this process identified most of the REST scans with the most severe artifacts, nonetheless, it should not be considered a complete, comprehensive list of all of the scans with severe artifacts. The list of scans with prominent artifacts will hopefully serve as a useful test-bed for testing de-noising algorithms.

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Issue code E: FIX Hand Reclassification of Signal Components
An evaluation of network matrices generated from each subject's rfMRI data before and after ICA-FIX processing (cleaning of artifacts) revealed some subjects across the entire HCP study with at least one rfMRI scan (run) that was not sufficiently cleaned by FIX as it was trained early on in the project (see ICA-FIX section of Ref Manual). Investigation of the signal components in the "uncleaned by FIX" scans revealed that some signal components identified by ICA-FIX were clearly noise components likely introduced by scanner coil element temporal instabilities. For these rfMRI scans, we manually reclassified one or more "signal" components as noise components and ran the ReApplyICAFIX pipeline to clean these data. Because the results are dependent on the rfMRI data, after this second round of FIX cleaning (reapplication of FIX with the hand reclassification), we also reran the RestingStateStats, MSMDeDriftAndResample, and MSMAll pipelines and replaced the outputs of these pipelines for the affected subjects.

Subjects who have had one or more rfMRI scan for which one or more FIX signal component(s) have been reclassified by hand to be noise components and had ICA-FIX reapplied are flagged with the issue code E for the QC_Issue measure. A list of these subjects and affected scans is also available on the QC Issues wiki. Note: All of the FIX hand reclassified QC_Issue E subjects are also flagged with issue code D.

 

Reference

Power, JD. A simple but useful way to assess fMRI scan qualities. Neuroimage. 2016 Aug 7. pii: S1053-8119(16)30387-1. doi: 10.1016/j.neuroimage.2016.08.009. [Epub ahead of print]