B0s in preprocessing

1

I separated my B0s from my diffusion weighted images in order to make a mean_B0 file. Then, I denoised & degibbed just the diffusion weighted images but not the B0s. Now, I need to do eddy correction on a single file containing my B0s and my diffusion weighted images. I have two questions, below. Any advice appreciated!

  1. should I have run the denoising & degibbing on a single file containing my B0s and my diffusion weighted images?

  2. is there a method for merging the B0s back with the denoised/degibbed diffusion images? The dirmerge command seems to be for merging directories rather than image files…

2

Yes! In particular, Gibbs ringing is much more pronounced on b=0 images, so it makes no sense to split them off. In general, all preprocessing steps should have the full DWI dataset as input. If you are unsure about the correct steps, please consult Preprocessing steps