MedSAM2 is not setting up Spatial Information

[morganrcu]

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

[rasakereh]

Thank you for bringing this to my attention. It was an issue with index offsetting which is fixed now!