Tips for semi-automatic segmentation of fetal brain MRI

Support
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1

Hello to all.
I’m trying to segment fetal MRI brains acquired with multiplanar T2-HASTE sequences (see an example below taken from Radiopaedia).

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I’m currently having a harsh time with manual segmentation which is really time consuming since I have to segment every slice and avoid CSF spaces and ventricles.
I tried with a seed based approach, also a threshold based one without success. I also tried using a registration based approach but the coregistered images are reformatted into a different plane and I can’t get access anymore to a standard axial plane.
Does anyone have any tips? Should I rely to a manual segmentation approach?

Thank you!

GMA

2

What exactly you would like to segment?

Seed based approach should work fine, maybe you could post a few screenshots that illustrate what problems you are running into.

If registration-based approach works better then you can use that. You can resample the image with image planes at arbitrary orientation (using Crop module or any of the resample modules).