FSL TOP UP on two dti scans

Hi FSL users,

any hint on how to use FSL topup on two phase encoded DTI scan each with 63 direction and 1 b0, the data is actually from PPMI dataset (PD patients) and am trying to correct for distortion using topup. I know it can be used for one DTI scan and 2 b0 but have no experience with two scans!

Thanks in advance


HI @bassamalfatly

Over and above the “interface simplification / automation” that dwifslpreproc provides (or at least claims to), the only time at which the outcomes of dwifslpreproc and manual execution of topup / eddy should deviate (assuming all other parameters are equivalent / correct) would be:

  • Images with an odd number of voxels in any spatial axis. dwifslpreproc applies image padding to alleviate a topup limitation in such cases, whereas without such, the advice is to use a different topup config file, and that may change the field estimate slightly;
  • Datasets where all DWIs were acquired with opposing phase encoding directions, since dwifslpreproc uses a different method for recombining those matched volumes in the output image.

all the best

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Hi @bassamalfatly,
I’m not familiar with the recommendation from @ZERAIIabdo so just answering from an FSL perspective… suggest that you follow the steps outlined on the FSL eddy user guide found here eddy/UsersGuide - FslWiki (but with caution because it says page is being edited in prep for next release). You basically extract your B0s from each DTI acquisition, temporally merge, run topup on those to estimate susceptibility induced off-resonance field, then apply that to the merged (2x) full acquisition using eddy. Hope that makes sense! All the best!


Hi @bassamalfatly
I have just implemented a new module called Module_pipeline_to_generate_FA_and_MD_maps in the software MP3 who does exactly that.
To be more precise, this module execute several function :
’ → A DWI denoising (MRtrix : dwidenoise)’
’ → A Gibbs ringing artifacts removal (MRtrix : mrdegibbs)’
’ → A DWI distorsion correction (MRtrix : dwifslpreproc)’
’ → A Mask estimation (MRtrix : dwi2mask)’
’ → A DWI upsampling (MRtrix : mrgrid)’
’ → A Tensor-derived parameter maps generation (MRtrix : dwi2tensor & tensor2metric)’

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