Description
The following is based on my experience with running T2w anatomical scans through version 22.0.6, but looking through the current code in the master branch, I don't see any reason to expect that it wouldn't be an ongoing problem with the current version.
This line of code
https://github.com/nipreps/mriqc/blob/24f786ae9e312b55830139e354627e837ea5703a/mriqc/qc/anatomical.py#L213C1-L213C16
defines the following mapping between the tissue labels used in MRIQC and the FAST segmentation labels:
FSL_FAST_LABELS = {"csf": 1, "gm": 2, "wm": 3, "bg": 0}
That mapping is indeed correct for T1w anatomicals. But at least in our T2w data, the typical segmentation that we are getting out of FAST (as launched by the MRIQC default settings) has GM = 1, WM = 2, and CSF = 3. But MRIQC doesn't appear to account for that altered mapping for T2w data.
The end result is that any MRIQC metric that is dependent on the T2w segmentation is either mislabeled, or just wrong (e.g., CJV and CNR are intended to be based on GM and WM, but per above what MRIQC is labeling "wm" is typically actually CSF, and what it is labeling "gm" is typically actually WM, in the case of T2w data).