Dwibiascorrect doesn't do a good job

#1

Hello all,

I used dwibiascorrect with -ant switch on my single shell dwi data but it data looks better without bias correction.
Please see before bias correction:

before
before.PNG1912x839 33.3 KB

and this is after:

after
after.PNG1913x838 30.9 KB

Any idea what’s going wrong?

Thanks,
Mahmoud

#2

This sounds suspiciously like this issue, which seems specific to MRtrix3 version 3.0_RC2. Which version are you using? In 3.0_RC3, the default parameters for the ants algorithm were adjusted, so it might work better in that version. In addition, support was added for overriding them on the command line, which should at least allow you to tweak the parameters to the underlying ANTs command, N4BiasFieldCorrection, to hopefully get a decent result.

#3

Thanks for your response.
Here is the version that I use:
MRtrix 3.0_RC3-83-g538f905c dwibiascorrect bin version: 3.0_RC3-83-g538f905c

Also, my data is from an infant cohorts.
Is there any any assumption in the pipeline that the data must be from adults? if so, where can I modify that?

Thanks,
Mahmoud