Hello everybody,

thanks again for providing the preprocessing scripts, they helped me to understand a lot.

But now I have a question: Is there an output-file being generated which is the original resting-state scan with all residuals removed but still remains in the exact same voxel-space as the original scan?

Before, I thought that rest_res.nii will be in the exact same space whereas rest_res2standard.nii would be the same result warped into standard MNI space. But if I compare rest_res.nii with the original scan, they seem not to be coregistered to the same space anymore.

As I would like to perform my calculations in subject space and e.g. use grey-matter masks derived from the original space, it would be great for me to have a volume without nuisance signals in the original subject space.

Thank you so much once more, for any suggestions!

Andreas

Hi Andreas,

the only difference between rest.nii.gz and rest_res.nii.gz orientation-wise, might be that rest.nii.gz is in RAI or ASL (or some other scanner-specific orientation), while rest_res.nii.gz has been oriented to RPI.

We apply the (re)orientation to RPI to both the anatomical and functional scan to make sure we are operating in the same (subject-) orientation. However, this should not be a problem for subject space calculations (in fact we try to use subject space calculations whenever possible). I would suggest to just reorient your grey-matter masks to RPI (or derive it from head.nii.gz which is the mprage.nii.gz reoriented to RPI).

Let me know if this is not working for you!
Maarten