Dear community,
I am currently using dwidenoise to process a set of diffusion images with 585 volumes acquired at different diffusion times for a rat brain. However, I have encountered an issue I hope you can help clarify.
When I apply the denoising with a kernel size of 9x9x9 (729>585), I notice that part of the brain remains undenoised (the voxels have the exact same value as before denoising). These are the voxels in the sigma map (orange map), which shows zero values. This behavior is unexpected since I am not using any mask, and I assumed the denoising would be applied across the entire image.
Interestingly, this region spans approximately 9 voxels along one direction, so as a workaround, increasing the kernel size to 11x11x11 resolves the issue:
Could you provide any insight into why this might be happening?
Thank you in advance for your time and help!
Rita