FSL: Useful commands

Create a spherical ROI using fslmaths:

fslmaths $FSLDIR/data/standard/MNI152_T1_2mm -mul 0 -add 1 -roi 50 1 50 1 50 1 0 1 point -odt float
fslmaths point -kernel sphere 9 -fmean sphereres -odt float

Note that in the first command I do "-mul 0 -add 1" to make sure that the whole image is full of zeros before adding one to the ROI.