SlicerMorph ImageStacks ROI transformation yields incorrect cropping

Community SlicerMorph
1

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
ROIissue_041020251920×1200 154 KB

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

2

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)

3

Thanks Murat! I’ll do the feature request.