registration overlay problem

[inbar meningher]

I create a segmentation based on the T1 image, when I save the segmentation to an NII and overlay it on the T1 image, they are not aligned (The red segmentation should be lower). why is that?

Thank you!

Inbar

[jonas bianchi]

Image is not showing, can you send a new ss?

[inbar meningher]

[inbar meningher]

[inbar meningher]

Can someone help?

I create a segmentation based on the T1 image, when I save the segmentation to an NII and overlay it on the T1 image, they are not aligned (The red segmentation should be lower). why is that?

[Dorian Pustina]

If I had to guess, the problem is you using MRIcron to check things out. Which means some sort of qform/sform header discrepancy in the T1 image, see here: https://github.com/ANTsX/ANTs/wiki/How-does-ANTs-handle-qform-and-sform-in-NIFTI-1-images%3F

You need to check if they are ok in itksnap.

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[Olena Tankyevych]

I am not sure it is the case here, but when it comes to overlay issues, which are common for me when using ITKSnap, I tend to think of this thread :

https://github.com/nipy/nibabel/issues/801#issuecomment-549134773

The solution I use is : c3d  -copy-transform or c3d -swapdim or even two of them, as Itksnap not only changes the original orientation, but also approximates the pixel dimensions, so when you verify if two images are aligned (one original and a segmentation from ItkSnap, for instance) in some other environment, then you might get errors.