FSL topup on two DTI scans?

10 November 2021 1 10K Report

Hi FSL users,

any hint on how to use FSL topup on two phase encoded DTI scan each with 63 directions and 1 b0, the data is actually from PPMI dataset (PD patients) and am trying to correct for susceptibility 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

Bassam

Martin Domin

Hi Bassam,

so there is 1 b0 volume in each phase encoding direction - hopefully 180° opposing? Then just calculate the topup distortion field with these 2 b0s and feed the result into eddy. Here you would use all of the data (b0_PED1+bXXX_PED1+b0_PED2+bXXX_PED2) of both PEDs concatenated into one file…

What you are looking for is the standard case for topup&eddy and well described on their user guide website.

Best,

Martin

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