Alignment/Skull stripping question


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 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!

Hi, Pascale-

I don’t see what the issue would be with aligning EPI->T1w_with_skull to get Transform_A, and then T1w_without_skull-> other image to get Transform_B. Then you can get EPI->other image via concatenating Transform_A and Transform_B. This works because the T1w space does not change depending on having the skull or not. And you will want to concatenate the transforms, anyways, because applying each separately to the EPI would lead to unnecessary and unwanted smoothing.

Does that seem reasonable?


For AEA, you may want “-child_anat mydset_with_skull” (replace that dataset name with the name of your dataset). That will just apply the same affine transformation to the original unskullstripped anatomical dataset. Or you can apply the transformation yourself with “3dAllineate -1Dmatrix_apply”.