How can I crop some CT data into same region?

Hi, I’m new to 3D slicer.

I have several series of CT data, like day0,1,… for each mouse.
I want to compare bone volume change over time.

I use “Expert Automated Registration” to align the orientations.

Then, I want to crop same region like below image.
Which tool is appropriate?

blue: day0
yellow: day1
red: day2
green: day3
black line: some regions I want to crop.(I will do it more accurately.)

you can crop it with the same ROI box.

Thank you for replying.

I tried that and I can.
Now my procedure is below.

Load series of DICOM data.
→ Use “Expert Automated Registration”, fix:day0 move:day1,2,3
→ Make Segmentations to see bone volumes(like the photo above.)
→ make ROI box and rotate it with “Transform”
→ Apply ROI box to original volume data with “Crop Volume”
→ Make Segmentations of cropped Volume.
→Calculate segment Volume with “Segment statistics”

It takes much time. Can I shorten these steps?
Also, is it possible to apply scissor tool(free form) simultaneously to these Segmentations?


You can write a short Python code snippet that performs all the steps automatically. You can run the code snippet using a keyboard shortcut (or if you want to have a more convenient GUI then create a Python scripted module). See lots of examples in the script repository. You can learn about basics of Slicer programming from developer tutorials.

As far as ‘crop some CT data into same region’ is concerned, you may get some insight from this module. It applies saved ROIs to crop CT volumes of known dimensions. You will obviously need more scripting for your requirements.

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Thanks a lot!
I will try to make python scripts.