open-discussion > Aligning ROI masks to structural space
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Feb 8, 2019  07:02 AM | Yizhou Wan - University of Cambridge
Aligning ROI masks to structural space
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
Feb 8, 2019  04:02 PM | mehrnaz jenabi
Aligning ROI masks to structural space
> Hi Yizhou
You can use one of the FSL tools for reorient your data or if you have AFNI you can run this:
3dresample -orient LPS -input your mask -prefix your out put
Good luck
Mehrnaz