Hi,
I'm testing MedSAM2 version on the segmentation of a brain tumor and I suspect there is some issue with how MedSAM2 processes origin and spacing information. I want to segment this bright structure:
I mark first and last slides and draw a ROI:
After segmenting middle slice, the result I obtain is on a different slice, shifted and is bigger than expected:
However, it has a nice shape. My feeling is that the origin and spacing information is not being properly setup on SAM2 output. These are the properties of the MRI volume:
Hi, I'm testing MedSAM2 version on the segmentation of a brain tumor and I suspect there is some issue with how MedSAM2 processes origin and spacing information. I want to segment this bright structure:
I mark first and last slides and draw a ROI:
After segmenting middle slice, the result I obtain is on a different slice, shifted and is bigger than expected:
However, it has a nice shape. My feeling is that the origin and spacing information is not being properly setup on SAM2 output. These are the properties of the MRI volume:
Here is the sample data:
https://drive.google.com/file/d/1DUV5wg5fPr8Hkj6MHNnSjsyrCD5TfWXn/view?usp=sharing
Do you think is an spatial metadata issue? Kind regards, Rodrigo