Dear MRtrix expert:
When I use this command, dwinormalise [ options ] input mask output,
dwinormalise dwi_denoised_unringed_preproc_unbiased.mif wm_mask.mif dwi_denoised_unringed_preproc_unbiased_normalised.mif -force
the output file without any value.
The terminal did not report an error.
here is the input file and output file.
There are no b=0 volumes in my file. It is the reason caused the problem?
I’ve just looked at the code for this, and yes, that would be the reason. As it says in the command synopsis, it looks for b=0 volumes, then computes the mean b=0 intensity for each voxel in the mask, which will give Not-a-Number due to the divide by zero.
More to the point though: these days we would advocate the use of mtnormalise to deal with both intensity normalisation and bias field correction – even for single-shell data where we’d advocate the use of multi-tissue CSD with WM & CSF responses only (see e.g. this post, amongst others). I think we’ll eventually end up removing