Dear Oskar,

On 11.07.2013, at 20:37, Oskar W <[log in to unmask]> wrote:

> 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'"

the error message tries to tell you that the first semicolon is misplaced. Move it before the `do´, as in `for … ; do … ; done´. There is also a $ missing before {g}_GM_… .


Regards,
Timm