# Workflow Advice: Preclinical rat brain CT hemispheric volumetry

**URL:** <https://discourse.slicer.org/t/workflow-advice-preclinical-rat-brain-ct-hemispheric-volumetry/48643>\
**Category:** Support\
**Created:** [October 29, 2026, 7:56pm UTC](https://discourse.slicer.org/t/workflow-advice-preclinical-rat-brain-ct-hemispheric-volumetry/48643 "2026-10-29T19:56:25Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![kbroeren](https://avatars.discourse-cdn.com/v4/letter/k/ecb155/32.png) [@kbroeren](https://discourse.slicer.org/u/kbroeren)\
**Post date:** [October 29, 2026, 7:56pm UTC](https://discourse.slicer.org/t/workflow-advice-preclinical-rat-brain-ct-hemispheric-volumetry/48643/1 "2026-10-29T19:56:25Z")

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Hello,

I am working with micro-CT scans of rat brains to quantify hemispheric tissue loss following Controlled Cortical Impact using the method: % Tissue loss = (Vcontra-V ipsi)/(V contra). There are three specific steps that I am looking for recommendations on.

1. Our scans are frequently off-center, which makes it hard to accurately split the brain into two hemispheres.

- What approach should I take to rotate/re-slice the volume before dividing it into the left and right hemispheres?
- Once it is aligned, is there an established way to define a cutting plane to partition the brain down the midsagittal plane?

1. Standardizing anatomical boundaries. The olfactory bulbs, and cerebellum were dissected prior to scanning, but some remnants remain.

- What tools are recommended to establish anterior/posterior cutoffs so that remnant tissue is excluded uniformly across all subjects?
- How do I do this without sacrificing some of the cortical area?

1. Suppressing Surface Spikes/Noise. Due to noise at the tissue boundary, intensity thresholding results in a jagged dorsal cortical surface rather than smooth contour.

- Which tool can I use to preserve the true cortex without distorting the lesion area?

Any advice helps!

Thank you