# Image Registration and Segmentation Across Modalities

**URL:** https://discourse.slicer.org/t/image-registration-and-segmentation-across-modalities/6469
**Category:** Support
**Tags:** segmentation
**Created:** [April 11, 2019, 2:01pm UTC](https://discourse.slicer.org/t/image-registration-and-segmentation-across-modalities/6469 "2019-04-11T14:01:24Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![MSpindler](https://avatars.discourse-cdn.com/v4/letter/m/77aa72/32.png) [@MSpindler](https://discourse.slicer.org/u/MSpindler)
#### Post date: [April 11, 2019, 2:01pm UTC](https://discourse.slicer.org/t/image-registration-and-segmentation-across-modalities/6469/1 "2019-04-11T14:01:24Z")

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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?

Cheers  
Melanie