# How to segment bad quality 4D MRI FLOW

**URL:** <https://discourse.slicer.org/t/how-to-segment-bad-quality-4d-mri-flow/47975>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [August 25, 2026, 12:48pm UTC](https://discourse.slicer.org/t/how-to-segment-bad-quality-4d-mri-flow/47975 "2026-08-25T12:48:49Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![VERRUCKT](https://avatars.discourse-cdn.com/v4/letter/v/22d042/32.png) [@VERRUCKT](https://discourse.slicer.org/u/VERRUCKT)\
**Post date:** [August 25, 2026, 12:48pm UTC](https://discourse.slicer.org/t/how-to-segment-bad-quality-4d-mri-flow/47975/1 "2026-08-25T12:48:49Z")

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Hi everyone 🙂

I’m working on aortic segmentation from 4D flow MRI. I’ve been using TotalSegmentator but results are poor, I assume mostly a domain issue, since it’s CT-trained, plus the low SNR of my data.

Two things I’d love input on:

**1. Anything off-the-shelf?** A pretrained model or pipeline I could run directly on my volumes, without annotating or training anything. Has anyone tried the MR variant of TotalSegmentator, or a pretrained nnU-Net for the aorta, on 4D flow data?

**2. If not, what’s the standard workflow?** I’d rather follow an established approach than improvise. Do people segment the magnitude images directly, or reconstruct a PC-MRA first? How many annotated volumes are realistically needed to fine-tune something usable? Any public 4D flow dataset with aortic labels?

Happy to write up whatever ends up working, in case it’s useful to others.

Thanks a lot!

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**Author:** ![Deep\_Learning](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/deep_learning/32/15345_2.png) [@Deep\_Learning](https://discourse.slicer.org/u/Deep_Learning)\
**Post date:** [August 26, 2026, 1:24pm UTC](https://discourse.slicer.org/t/how-to-segment-bad-quality-4d-mri-flow/47975/2 "2026-08-26T13:24:14Z")

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nninteractive. there is an extension