Hi Matthew,
I actually just got it to work by changing all of the T1 volume titles from starting with numbers (e.g., 101.MPRAGE.nii.gz, 102.MPRAGE.nii.gz) to starting with a consistent letter (e.g., S101.MPRAGE.nii.gz. S102.MPRAGE.nii.gz). I have no idea why that made things work, but it did! Sorry for the bother!
Best,
Dave
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