Colin Hansen

What is the resolution of your DWI?

This matches some of the data we used to test the generalizability of the model, so I don't think you should have any issues.

Hello Johannes, Can you also share images of 1) the raw b0, 2) b0_all volume 1 and volume 2, and 3) b0_all_topup volume1 and volume 2? Also it may help...

So it looks like something is wrong with output of topup. Volume 1 in b0_all_topup definitely looks distorted in some way. Can you include the output of fslhd? It may...

I can't find anything obviously wrong in the header info. If you are able to share your data, could you provide a way for me to grab the b0 and...

Hello Jayashree, I want to make sure I understand correctly. You are comparing the results from topup run with your b0 and the synthetic b0 within the synb0 pipeline to...

I believe our container uses FSL 5.0.10, but I don't think there will be any significant differences in the topup or eddy methods between versions. I have not looked in...

In the paper, MSE was calculated for FA not the diffusion signal itself. The FA calculation and MSE were done with in house MATLAB code written by the primary author....

The error was calculated voxel-wise within the brain volume. If you want to separate by region, I would first calculate the squared error and then use whatever masks you like...

Hello Johannes, We decided the easiest solution would be to allow users to optionally provide their own mask. I've updated the source code as well as the docker, so that...