SOLVED - A colleague advised me, the dti_motion_do_all script should read:
#!/bin/sh
#Get motion information for each subject in each of the two datasets, using Mark's script, called dti_motion
cd /imaging/cr01/PD_DTI/C_10/12x5
/home/cr01/bin/dti_motion C10_12x5ec.ecclog
cd /imaging/cr01/PD_DTI/C_10/30x2
/home/cr01/bin/dti_motion C10_30x2ec.ecclog
#End of script
I just needed to explicitly tell the shell where to find the dti_motion script. This now works
Also, in case any other linux newbies find it useful, a looped version would look like this:
#!/bin/sh
#Get motion information for each subject in each of the two datasets, using Mark's script, called dti_motion
for i in {11,12} <--numbers of your directories
do
for j in {12x5,30x2} <--numbers of your directories
do
cd /imaging/cr01/PD_DTI/C_${i}/${j}
/home/cr01/bin/dti_motion C${i}_${j}ec.ecclog
done
done
#End of script