Hi Sue,
I think you can use the fsl script called "fslroi":

$ fslroi "input" "output" "xmin" "xsize" "ymin" "ysize" "zmin" "zsize"
$ Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension.

I.E. fslroi my_T1 my_T1_cutted 0 -1 0 -1 40 -1
my_T1_cutted will retain X and Y dimension while it will be cutted in Z dimension about 40 slices.

Hope this help
Cheers

Matteo