Using FSL and MRtrix3 for TBSS analysis

1

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:

-TOPUP

-Eddy correction

-DTIFIT

-TBSS

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.

Benxa.

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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)

-GIBBS RING REMOVAL (mrdegibbs)

-TOPUP

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

-DTIFIT

-TBSS

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,

Manuel

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