I’m working on warping ROIs from MNI space to a subject’s native FA space using ANTs and MRtrix. After applying transformations, I noticed that while the right ROI looks normal (intensity values ranging from 0 to 1), the left ROI has intensity values ranging from 0 to -1, which is unexpected. I cannot view the left ROI despite the right looking great and co-registered.
Here are the steps I followed:
- Registered subject’s FA image to MNI152 template using
- Applied inverse transformations to warp the ROIs from MNI to FA space.
- For registration:
antsRegistrationSyN.sh -d 3 -f [MNI] -m [FA] -o output
- For warping:
antsApplyTransforms -d 3 -i [ROI] -r [FA] -o [output_ROI] -n NearestNeighbor -t [Affine,1] -t [InverseWarp]
I’ve double-checked the original ROI files, and both appear normal in MNI space. The issue only arises after transformation. I’ve also tried re-running the transformation steps, ensuring that all parameters are identical for both ROIs.
Has anyone encountered a similar issue, or can anyone suggest what might be causing this discrepancy in intensity values for the left ROI?
I’m using the most recent ANTs version and MRtrix 3.0.4 on a macOS M1 system.
Thanks in advance for any insights or suggestions!