Hi, 

How can I align ROI masks to structural images?

I have a structural MRI sequences for each of my brain tumour patients  coregistered to the T1C sequence. I then performed an affine 12 dof registration to a SRI24 atlas using FSL flirt. With these registered images I generated tumour masks using a automated segmentation process- Deepmedic. The outout tumour masks are not aligned to my input images (images after registration to atlas) so I cannot view them as an overlay on the input image.

I think it may be because the input images were in Neurological LPS- voxel orientation and RAS world orientation. The tumor masks are now radiological, LAS voxel and RAS world. The image and tumour mask transformation matrices are quite different. How can I put them in the same space?

Thanks