I am confused that how to align the brain.img with my functional data in spm...

https://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting

Best wishes!

1. Convert the brain.mgz volume to analyze:

mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img

2. Align brain.img with your functional data in spm (eg, func.img)