Hi Rob and Alistair,
Thanks for getting back to me. I think I know how to do the transformation after the 5TT now with the code you sent, Alistair. However, while trying to figure it out I read more about the 5TTgen scripts and was wondering if I actually did the right thing to start with. I initially ran it with 5ttgen fsl which worked fine, however I used the T1 image that was generated with freesurfer during recon-all. Do I actually have to run recon-all at all if I use the 5ttgen fsl script or is it enough to provide the raw T1 image (generated from the DICOMs)?
Cheers, Lena