Banding in output

[andrew-taylor-2]

Hello! First off, thanks for this software!

Sorry if this is inappropriate for Github issues, but my problem is probably not so much an issue with the code as a request for reconstruction parameters.

The attached image is my current best reconstruction from 3 acquisitions -- 1.6 x 1.6 x 5mm, 1.6 x 5 x 1.6mm, and 5 x 1.6 x 1.6mm (i.e a sagittal 2d, a coronal 2d, and an axial 2d). To my knowledge there is no slice gap. The brain scans I'm using are from an adult. I used only niftymic_reconstruct_volume, with parameters --reconstruction-type HuberL2 --isotropic-resolution 1.6 --interleave 1.

As you can see, there is a certain variation in intensity across slices, especially along the A/P direction. I'm not sure if this intensity variation affects the whole slice. I just started a run with --intensity-correction 0, just in case this is the issue. The parameters mentioned above all helped to lessen this effect, but it's still there.

I saw another user in the issues saying that he had good results in a similar use case, but with 8mm slices. So I feel that if I had a better idea of what parameters to use, I could probably achieve better results.

Also, I have multiple subjects with the same type of scans, and they all experience this banding.

Thank you so much for reading! Let me know if it would be helpful to give some more details.