Hello!
I’m wondering if there is a way to align an EPI and a T1 dataset without skull stripping the T1.
We need to align EPI and T1 datasets to use for TMS localization, but for the TMS part, to perform the MRI to head registration, we need the T1 to have its skull. I tried a bunch of options with align_epi_anat.py but could not get as output a T1 aligned with its skull. I was wondering if perhaps I was missing something.
I know the manual nudge function could be used, but I was hoping not to have to align manually.
Thanks a lot in advance!
Pascale
