Dear AFNI expert,
We recently used 7 T MRI focusing on the basal ganglia.
Because I never had experience in preprocessing 7 T images, I have a lot of questions for preprocessing.
First of all, the attached image (OriginalvsUnifized) shows how T1 has been changed after using 3dUnifize.
After this, I would like to remove the skull, but the algorithm does not work well due to background noise.
Normally, in the 3 T image, there was no signal in the background (black), but here as you can see there are a lot of noises in the background.
I think this is why a vanilla version of 3dSkullStrip does not work.
Second, we achieved 1.1 mm isotropic resolution while focusing on the basal ganglia with narrow FOV.
For the registration between EPI and MPRAGE, should we need to use the same slab for the MPRAGE?