Using FSL and MRtrix3 for TBSS analysis

Dear experts

I am currently working in the field of aging. I belong to an incipient group with little experience in handling neuroimaging data. I am currently trying to establish a protocol for DTI image analysis, specifically I am interested in carrying out a TBSS analysis. So far I have managed to perform TBSS analyses using only FSL by following this steps:


-Eddy correction



Are there any further steps you recommend? I have seen that MRTrix allows to perform some major steps to correct the images such as denoising, but I don’t know in which step of the proposed protocol I should apply them (before/after TOPUP) or if it really makes sense in the context of TBSS. Another question I have is if there would be any problem when converting .mif files to .nii (with the intention of creating a protocol that alternates FSL and MRTrix). Any help would be very appreciated.

Best regards.


Hi @benxamin ,

You are right, MRtrix allows you to do denoising and removing the gibbs rings artifacts. Your protocol would read something like this:

-DENOISING (dwidenoise, always as a first step)



-Eddy correction (using eddy and the output of topup)



The two steps will improve the quality of the processing and help you to create better maps.

MRtrix allows you to work as well with nifti images. I usually work with nifti because like you, I have to change a lot between MRtrix and FSL. What I do is to use the option -fslgrad when needed in MRtrix. I hope this helps.

Best regards,


1 Like