Kurt Schilling

Hi Hannes - you are right, I don't quite like what is happening in the brainstem. We generally go through a few steps to debug. First - it is hard...

Hmmm - I am also not entirely content with these results. The synthesized image seems to be OK, although I agree the brainstem loses a bit of contrast. It is...

Hi @araikes - hope I can help debug! A few questions: First (this probably isn't the issue), was the T1 pre-processed in any way? Some denoising algorithms, and even FreeSurfer...

Yes - this is still entirely possible to use. In fact, it doesn't really matter what the total readout time is, all that matters is that topup will try to...

Hi Fiona and all - great suggestion. We have now reflected this in the README. Also - I apologize for the delayed response!

> Hi @hanscol > > I'm having a similar issue as described above. My input directory contains the following files: "acqparams.txt" "b0.nii.gz" "T1.nii.gz" My output directory contains the following files...

> Hello from US. > I have the same issue Can you please copy the log messages printed in your terminal to help us debug? The most common failures are...

> Hi I am a neuroradiologist in France, I have the same problem. I don't understand what you mean about "provide the entier output log as a txt file". And...

Currently there is not. We recommend supplying a 3D b=0 image volume (b0.nii.gz) to the container and it will successfully work. Thank you, Kurt

There are two options. I would recommend just extracting the first volume from your b=0 image. This can be done using any toolkit - Matlab, python (DIPY), MRTrix3 (dwiextract), or...