For run_first_all you should use the original non brain extracted T1 images.
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide "The argument -i specifies the original T1-weighted structural image (only T1-weighted images can be used). "
If you use a brain extracted image as input, you should use the -b option. However, I think you should try to run FIRST on the non brain extracted data first.
Best Regards,
Gabor
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