Hiya, I’m running fMRIPrep 21.0.1 on multiband, multiecho data and seeing some repeated problems in my data. Looked at Poor fMRI Prep Brain Masks and some other posts but not sure if mine is the same issue.
(1) Brain masks for the functional data are erroneously including areas of signal outside the brain (this was also an issue in subjects previously preprocessed using fMRIPrep 1.4.1).
SDC results:
(RMET run2)
(rest)
CompCor results:
(RMET run2)
(rest)
(2) The preprocessed MNI-space optimally combined image (& its mask) also includes areas outside of the brain, though not necessarily the same areas (you can see this in the first CompCor figures). The T1w brain mask looks fine.
FYI: T1w images were defaced using pydeface prior to fMRIPrep. Also prior to fMRIPrep, we set the echo-1 PA scan to be the topup for all four echos in that run. (see below, from our manual)
We are collecting short top-up scans with the opposite phase encoding direction to the main runs (PA/FH instead of AP/HF) for each task, in order to apply pepolar SDC (see API — fmriprep version documentation). To do this, we just need to let fmriprep know which top-up scans are ‘intended for’ [distortion correcting] which functional runs. Since it is not optimal for apply different transformations to different echos (see Blipup Blipdown distortion correction on multiecho data - #2 by handwerkerd), we will set the echo-1 PA scan prior to each run to be the top-up for all echos in that run. This is done by adding an ‘IntendedFor’ field to the relevant .json sidecar files for the echo-1 PA fieldmaps. E.g., for sub-060:
[in fmap/sub-060_task-faceStroop_dir-PA_run-01_echo-1_epi.json:]
“IntendedFor”: [“func/sub-060_task-faceStroop_dir-AP_run-01_echo-1_bold.nii.gz”,
“func/sub-060_task-faceStroop_dir-AP_run-02_echo-1_bold.nii.gz”,
“func/sub-060_task-faceStroop_dir-AP_run-01_echo-2_bold.nii.gz”,
“func/sub-060_task-faceStroop_dir-AP_run-02_echo-2_bold.nii.gz”,
“func/sub-060_task-faceStroop_dir-AP_run-01_echo-3_bold.nii.gz”,
“func/sub-060_task-faceStroop_dir-AP_run-02_echo-3_bold.nii.gz”,
“func/sub-060_task-faceStroop_dir-AP_run-01_echo-4_bold.nii.gz”,
“func/sub-060_task-faceStroop_dir-AP_run-02_echo-4_bold.nii.gz”],
Compressed directory with two output & reports from two representative subjects here:
sub-003 has the affine tolerance problem, sub-005 has the brain mask issues (particularly on functional runs “rest”, “RMET run1”, “RMET run2”, and “faceStroop run2”).
(I’d also love to understand what is causing these issues, just out of curiosity. I’d say the brain mask issue is happening on at least one run for a majority of subjects.)
Thanks for any help!
If the latter, could you confirm which files for which I copy the affine (a) from and (b) to using use 
(thank you!!)