# Creating ROI box markups in image coordinates (rather than anatomical coordinates)

**URL:** <https://discourse.slicer.org/t/creating-roi-box-markups-in-image-coordinates-rather-than-anatomical-coordinates/43393>\
**Category:** Support\
**Created:** [June 17, 2025, 4:44pm UTC](https://discourse.slicer.org/t/creating-roi-box-markups-in-image-coordinates-rather-than-anatomical-coordinates/43393 "2025-06-17T16:44:32Z")\
**Posts on this page:** 1\
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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:** [September 27, 2025, 8:12pm UTC](https://discourse.slicer.org/t/creating-roi-box-markups-in-image-coordinates-rather-than-anatomical-coordinates/43393/11 "2025-09-27T20:12:48Z")

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for posterity this feature is now implemented in slicer, and part of the `CropVolume` module since Sept 21s.

> <https://github.com/Slicer/Slicer/pull/8737>
>
> Orientation of the input volume can now be easily fixed in Crop Volume module us…ing the new "Reorient volume" section.
> 
> Options are added to tune "Fit to volume" beheavior. It is now possible to align the cropped volume's ROI to the world coordinate system (or keep the current ROI orientation). This is useful if the user wants to align the cropped volume axes to the world coordinate system, for example to make segmentation in anatomical planes easier.
> 
> fixes #8415
> 
> \<img width="1282" height="1027" alt="image" src="https://github.com/user-attachments/assets/270c25cf-7b08-4f5d-9ac1-1da266aa824f" /\>
> 
> @muratmaga

To align your volume with anatomical planes, hit expand “reorient volume” tab, then use the widgets to transform your volume and harden it to finalize. If you want to create a new volume that’s in inline with the world axes, choose the `Align to world axis and resize` from the new drop down associated with Fit to Volume button. This will resample the oriented volume into the new grid and save the output to the output volume.

thanks for @lassoan implementing this.

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