I just ran into the exact same problem; it's been a while since your question, but hopefully this will help others.
"filename_brain.nii.gz" is supposed to be the brain extracted image (no skull), whereas "filename.nii.gz" is the original image (with skull).
The wording in the MELODIC tooltip is a bit vague, and I initially interpreted it the same way that you did ("filename_brain.nii.gz" is the non-brain-extracted image).
Quoting the tooltip:
if you turn on nonlinear registration, FEAT will look for the original non-
brain-extracted structural and standard space images in the same
directory as the brain-extracted images that you input into the GUI,
and with the same filename except for the "_brain" at the end.
"with the same filename except for the "_brain" at the end"
can be interpreted by people new to MELODIC/FNIRT as a requirement to add "_brain" to the file names they already had listed as main structural images.
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