# SlicerMorph ImageStacks ROI transformation yields incorrect cropping

**URL:** <https://discourse.slicer.org/t/slicermorph-imagestacks-roi-transformation-yields-incorrect-cropping/42525>\
**Category:** SlicerMorph\
**Tags:** slicermorph\
**Created:** [April 10, 2025, 3:53pm UTC](https://discourse.slicer.org/t/slicermorph-imagestacks-roi-transformation-yields-incorrect-cropping/42525 "2025-04-10T15:53:40Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![scutisorex](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/scutisorex/32/77239_2.png) [@scutisorex](https://discourse.slicer.org/u/scutisorex)\
**Post date:** [April 10, 2025, 3:53pm UTC](https://discourse.slicer.org/t/slicermorph-imagestacks-roi-transformation-yields-incorrect-cropping/42525/1 "2025-04-10T15:53:40Z")

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Hi all,

I’m using ImageStacks to import ROIs of some larger CT stacks. I specified my ROI using Markups and transformed it to include only the portion of the scan I wanted (skull of the animal, see below). This included rotating the ROI out of the plane of the slices. However, when I did the subsequent ROI import at half resolution, it didn’t keep everything inside the ROI, and kept some of what I didn’t need (especially visible in the green slice and 3D view):

 ![ROIissue_04102025](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/5/b58bcf8d388b7e8075c5c109f70b27c89eb12089.jpeg)

Any thoughts on why this occurred? Does the module have the capability to include just parts of a slice? I feel like I’ve had no issue with this in the past.

Many thanks for any insights here!

**Operating system:** Windows 10  
**Slicer version:** 5.8.1  
**SlicerMorph Version:** 172e036

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [April 10, 2025, 4:00pm UTC](https://discourse.slicer.org/t/slicermorph-imagestacks-roi-transformation-yields-incorrect-cropping/42525/2 "2025-04-10T16:00:33Z")

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> [@scutisorex](#):
>
> Does the module have the capability to include just parts of a slice?

I don’t think ImageStacks currently support cropping the volume while importing under a transformed ROI. If that’s what you want to do, you need to use the regular `Crop Volume`.

Also, if you can a feature request for this on the SlicerMorph github page, we might consider implementing (at some point)

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**Author:** ![scutisorex](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/scutisorex/32/77239_2.png) [@scutisorex](https://discourse.slicer.org/u/scutisorex)\
**Post date:** [April 10, 2025, 4:01pm UTC](https://discourse.slicer.org/t/slicermorph-imagestacks-roi-transformation-yields-incorrect-cropping/42525/3 "2025-04-10T16:01:15Z")

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Thanks Murat! I’ll do the feature request.