atlas question

[amirro1]

Hello,

Thanks again for this tool. I was wondering how you aligned your T1 images to atlas (and specifically which atlas space/ template was used). I am asking because it seems that the orientation of the atlas has an effect on the predictions. (Since slicer.py saves the niftis into jpg images, the initial orientation of the nifti effects how these jpgs are written out)

Thanks,
Amy