Hi,
this should be easy but I simply cannot get this to work. I want to align a bunch of NIFTI files (beginning with mwr*) to MNI 2 mm resolution, while renaming them (adding the suffix _GM_to_template_GM_mod) and moving them to subdirectory struc. I tried this:
for g in `$FSLDIR/bin/imglob mwr*` do ;
$FSLDIR/bin/flirt -in ${g} -ref $FSLDIR/data/standard/MNI152_T1_2mm –applyxfm -usesqform -out struc/{g}_GM_to_template_GM_mod;
done
and got the output: "-bash: syntax error near unexpected token `flirt'"
What am I doing wrong?
Cheers,
Oskar W
M.Sc. Eng.Phys.
Lund University
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