open-discussion > Aligning ROI masks to structural space
Showing 1-2 of 2 posts
Feb 8, 2019 03:02 PM | 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
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 9, 2019 12:02 AM | 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
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