MRI Segmentation in the Wrong Orientation


My issue is two-fold: first -- my anatomy volumes (MRI) are loading in the wrong orientation. The Axial view is rotated 90 degrees. I corrected this by rotating the MRI before loading the rest of the surfaces, but my atlases are still rotated 90 degrees. This is leading to an error that states the dimensions of the volumes do not match. I know my segmentation is clean as I am viewing them on Freesurfer right now. The second, and arguably more important issue is that my subcortical structures are misaligned when merged with the cortex. How should I proceed?

Thank you,


Hi @ethanberi

It is hard to guess what the issue is from your description.

Can you share some screenshots of the MRI viewer? and the surfaces.

How did you change the rotation of the MRIs?

what volume?

so if something is wrong in the first steps, it will be also wrong on the other steps.

We need first to understand the origin of the error.

Do you have the original MRI file?