I am using the following command for creating the DWI brain mask:
dwi2mask IN/dwi_denoised_unringed_preproc_upsampled.mif IN/dwi_mask_upsampled.mif
However, it seems that the output is not binary, please see below:
Is that normal or the output should be a binary mask?
Also, I used FSL BET to create my own mask which looks like below:
Which mask looks more appropriate to be used with dwi2fod?
I think there is nothing to worry about here, this is a visualization “problem” only, if you untick the box interpolate, you’ll see how the mask is binary. MRtrix by default interpolates the images. I hope this helps.
So you confirm that the output of dwi2mask is/should not be binary?
Any idea about which of the the two masks is better?
Sorry for the confusion, the mask is binary, but it doesn’t look binary only for the interpolation. If you untick the interpolation box you’ll see how the mask is binary. Which one is better all depends how they look overlaid to your image, or what are you trying to attempt.