Hi, I am interested in getting 3D box annotations in MRI data. ROI markups appear to be a good fit for this but the current behaviour is counterintuitive to users. In particular, they got confused by getting forced into creating “skewed” boxes, see snapshot below: [Screenshot 2025-06-17 at 10.37.…

Good point! Most of the time users would probably want to place the ROI with axes aligned with the slice view axes, so probably we should change the placement behavior (instead of making it configurable). @muratmaga would this behavior would be an improvement for your workflows, too?

[image] lassoan: @muratmaga would this behavior would be an improvement for your workflows, too? For us the biggest improvement would come enabling easier linear resampling after we manually align our microCT scans (which is the linked issue). If it is possible to do that both, that would be …

[image] muratmaga: If you create ROI inside the Volume Rendering module, it will be aligned with respect to your rotated MRI image (and not be skewed) like that. I’m not sure I understand the suggestion. The behaviour is the same if I initiate the ROI markup in the volume rendering view. The …

[image] lassoan: Good point! Most of the time users would probably want to place the ROI with axes aligned with the slice view axes, so probably we should change the placement behavior (instead of making it configurable). That default behaviour would be great for us. I am currently thinking …

[image] tvercaut: I’m not sure I understand the suggestion. The behaviour is the same if I initiate the ROI markup in the volume rendering view. No, use the crop volume feature in the volume rendering module to create the ROI. Not the markups one.

[image] muratmaga: No, use the crop volume feature in the volume rendering module to create the ROI. Not the markups one. I found a crop volume module but no crop volume function in the volume rendering module: Crop Volume — 3D Slicer documentation I as…

See the screenshot for crop volume functionality in volume rendering. [image] It is the same ROI markups initialized different. I agree it is cumbersome. I only offered this since it is available to do what you want to do right now (as opposed to wait for implementation, and funding for it).

Ah yes, clicking “Enable” and “Display ROI” next to “Crop” in the “volume rendering” module also works, albeit for a single box ROI. The path through the “crop volume” module allows creation of multiple box ROIs.

for posterity this feature is now implemented in slicer, and part of the CropVolume module since Sept 21s. ENH: Add volume reorientation to Crop Volume module main ← lassoan:crop-volume-reorient op…

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

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muratmaga (Murat Maga) June 17, 2025, 4:48pm 2

If you create ROI inside the Volume Rendering module, it will be aligned with respect to your rotated MRI image (and not be skewed) like that. There is sort of a related issue here:

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

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