Import problem - MITK to Slicer

Support
1

Operating system: Win 10
Slicer version: 4.9.0
Expected behavior: Trying to import segmentations I made in MITK into slicer
Actual behavior: Segmentations become ‘jaggedy’ - see screen grab below, particularly occipital and temporal lobes. Would greatly appreciate help with this as I don’t want to manually fix all these contours :roll_eyes: Any ideas what I might be doing wrong? I’m thinking the axis of the MRI is different from the axis of the segmentations. Is that something I can change in slicer?

Many thanks!

MITK
MITK1018×869 89.5 KB

2

How did you save the segmentation in MITK? As an image volume or as a surface meshes? Would you like to just visualize segmentation or further edit it?

3

I did a bit more general digging and noticed this button:

aligned
aligned711×335 41.8 KB

Problem fixed with a single click! Wish it was a bit more emphasised :slight_smile:

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