ok, i figured it out, had to be short... sigh, i want to hide in the ground
or something now... :)
anyway, here is the script which other people might find useful:
#!/bin/bash
echo "1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1">eye.mat
for i in m*.img
do
base=`echo $i | sed 's/.img//'`
short="i$base"
echo "Converting floating point $i to short"
flirt -datatype short -in $i -ref $i -applyxfm -init eye.mat -out
$short
rm -rf eye.mat
done
exit
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