for stuff in things
do
( something
  with
  stuff ) &
done
wait # for all the something with stuff

Whether it actually works depends on your commands; I'm not familiar with them. The rm *.mat looks a bit prone to conflicts if it runs in parallel...

for stuff in things
do
sem -j+0 ( something
  with
  stuff )
done
sem --wait

This will use semaphores, parallelizing as many iterations as the number of available cores (-j +0 means you will parallelize N+0 jobs, where N is the number of available cores).

sem --wait tells to wait until all the iterations in the for loop have terminated execution before executing the successive lines of code.

Note: you will need "parallel" (sudo apt-get install parallel).

Sample task

task(){
   sleep 0.5; echo "$1";
}

Sequential runs

for thing in a b c d e f g; do 
   task "$thing"
done

Parallel runs

for thing in a b c d e f g; do 
  task "$thing" &
done

Parallel runs in N-process batches

N=4
(
for thing in a b c d e f g; do 
   ((i=i%N)); ((i++==0)) && wait
   task "$thing" & 
done
)

It's also possible to use FIFOs as semaphores and use them to ensure that new processes are spawned as soon as possible and that no more than N processes runs at the same time. But it requires more code.

N processes with a FIFO-based semaphore:

open_sem(){
    mkfifo pipe-$$
    exec 3<>pipe-$$
    rm pipe-$$
    local i=$1
    for((;i>0;i--)); do
        printf %s 000 >&3
    done
}
run_with_lock(){
    local x
    read -u 3 -n 3 x && ((0==x)) || exit $x
    (
    "$@" 
    printf '%.3d' $? >&3
    )&
}

N=4
open_sem $N
for thing in {a..g}; do
    run_with_lock task $thing
done 

It seems the fsl jobs are depending on eachother, so the 4 jobs cannot be run in parallel. The runs, however, can be run in parallel.

Make a bash function running a single run and run that function in parallel:

#!/bin/bash

myfunc() {
    run=$1
    kar='KAR5'
    mkdir normFunc
    fsl5.0-flirt -in $kar"deformed.nii.gz" -ref normtemp.nii.gz -omat $run".norm1.mat" -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 
    fsl5.0-flirt -in $run".poststats.nii.gz" -ref $kar"deformed.nii.gz" -omat $run".norm2.mat" -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 
    fsl5.0-convert_xfm -concat $run".norm1.mat" -omat $run".norm.mat" $run".norm2.mat"
    fsl5.0-flirt -in $run".poststats.nii.gz" -ref normtemp.nii.gz -out $PWD/normFunc/$run".norm.nii.gz" -applyxfm -init $run".norm.mat" -interp trilinear
}

export -f myfunc
parallel myfunc ::: run2 run3 run4

To learn more watch the intro videos: https://www.youtube.com/playlist?list=PL284C9FF2488BC6D1 and spend an hour walking through the tutorial http://www.gnu.org/software/parallel/parallel_tutorial.html Your command line will love you for it.