# Multiple organs segmentation in a MRI sequence?

**URL:** https://discourse.slicer.org/t/multiple-organs-segmentation-in-a-mri-sequence/46699
**Category:** Support
**Tags:** segmentation, nifti, dce, multivolume, 4d
**Created:** [April 9, 2026, 1:36pm UTC](https://discourse.slicer.org/t/multiple-organs-segmentation-in-a-mri-sequence/46699 "2026-04-09T13:36:47Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![koperkill](https://avatars.discourse-cdn.com/v4/letter/k/cc9497/32.png) [@koperkill](https://discourse.slicer.org/u/koperkill)
#### Post date: [April 9, 2026, 1:36pm UTC](https://discourse.slicer.org/t/multiple-organs-segmentation-in-a-mri-sequence/46699/1 "2026-04-09T13:36:47Z")

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Hello,

For a DCE-MRI study, I would like to extract the signal intensity, through time, for a dozen organs and regions of the upper body.

I have successfully built a time sequence using my 40 volumes in time, drawn a segmentation mask for a single ROI, and experimented with the automatic segmentation with the excellent tutorial provided by @lassoan at [Automatic segmentation of sequences in time](https://discourse.slicer.org/t/automatic-segmentation-of-sequences-in-time/20756) , successfully propagating the registration through time.

This works with some success for bigger structures, but finer ones likes arteries and veins occasionally suffer from very bad registration; registration translates my veins into other organs for a few volumes, yet works fine for most of them…

I’m inclined to think that drawing more regions would add physiologically sound constraints on the registration, thus avoiding a transformation that misplaces, for example, the liver outside of the body, but this is purely speculative.

Finally, here is my questions:

- How would one solve this specific problem?
  - Should each organ be separately segmented or all should be done simultaneously as I suspect?
  - If registration of ROI works on most volumes, is it possible to manually adjust the few that do not align well?
  - Is there a hidden functionality that I’m not aware of for this specific problem?

Looking forward to reading your ideas! Thank you for your help