Dwi2response dhollander errror

Hi MRtrix community,

I have been trying to run the dwi2response dhollander command and have ran into a few errors regarding ?empty mask. I have created my own mask with dwi2mask and inserted it into the command, however mrtrix is still not using the provided mask and instead generating a new one, resulting in the same error message. If anyone has insight on what to do it would be much appreciated! Thanks in advance!

Command: dwiresponse dhollander -mask mask.mif input.mif out_wm.txt out_gm.txt out_csf.txt

Error message:
mrstats: [ERROR] Cannot output statistic of interest; no values read (empty mask?)
dwi2response: [ERROR] Error trying to calculate statistic ‘median’ from image ‘safe_sdm.mif’


Hi Perri,

It seems the problem is that you “start” with the mask (dwi2response — MRtrix 3.0 documentation)


dwiresponse dhollander input.mif out_wm.txt out_gm.txt out_csf.txt -mask mask.mif


Hi William,

Thanks so much for your reply!
I have tried the command again with the -mask at the end as well, and unfortunately I receive the same error message.

Warm regards,

I take it that you ensured that the mask contains of zeros an ones, is a 3d volume and fits the dwi data?