Image Registration and Segmentation Across Modalities

Dear Slicer community,

i plan on doing slice-by-slice segmentation of subcortical structures using T1,T2, and diffusion direction information. I want to start by aligning the individual brain in the midsagittal plane and in AC-PC in all modalities.
If I use these aligned images as input for Slicer, drawing on one slice produces a segment covering three slices (the one before and after my current slice).
As far as I understood, I can prevent this with the “Rotate to volume plane” option. But this way, the aligned image is of course shifted back into its inherent position, but I want to segment in AC-PC orientation.
How can I do the AC-PC alignment in Slicer itself to get five images (t1,t2,dti,tissue probability maps) in the same orientation (for overlays) and still be able to do the segmentations without spreading to other slices?
I also have the reorientation matrix to do this automatically, but I dont know where to put it.

Maybe someone knows which module is the right choice for that?