Hi Live,

Your for loop has some syntax issues. It should look more like this: 

#!/bin/bash
export ID_file= id_mTBI.txt
SUBJ_IDs=$(cat $ID_file)
for ID in $SUBJ_IDs ; do
./dke /home/eikeliv/Documents/MILD_TBI_DKE/${ID}/${ID}.dat
Done

Regarding the making of your .dat files automatically try using the "sed" command to replace strings within a file.  
Try searching some forums on scripting in bash for specific examples! 

Best,
Emilie