This protocol has been moved here

Correct for EPI induced susceptibility artifacts — this is particularly an issue at higher magnetic fields.

• If you have two opposing b0s and a sufficient amount of diffusion directions obtained, you may use FSL’s TOPUPand EDDY for distortion correction.
• If a fieldmap has been collected along with your data, FSL’s FUGUE tool may help compensate for the distortions.
• Alternatively, a subject’s DWI images can be adjusted through high dimensional warping of the b0 to a high-resolution structural (T1- or T2- weighted) image of the same subject not acquired using EPI. This requires multiple steps:
  • Make sure skull-stripping has been performed on both b0 and T1-weighted scans.
  • Make sure T1-weighted scans have undergone inhomogeneity (NU) correction.
  • Make sure T1-weighted scans and the DWI are aligned!! Check for L/R flipping!!
  • Linear registration of b0 of DWI and T1-weighted reference together. Due to differences in resolution and further registrations needed throughout the workflow we recommend initially aligning the the T1-weighted scans to ICBM space (which is the space of the ENIGMA-DTI template), then using a linear registration (with NO sheering parameters) to align your b0 maps to their respective T1-weighted scans in ICBM space
  • If using FSL’s flirt for linear registration, sheering can be avoided by manually setting the degrees of freedom (default 12) to 9 (flirt -in b0.nii.gz -out b02T1w.nii.gz -df 9 -ref T1w.nii.gz)
  • Once images are in the same space and linearly alight (visually check this!), you can perform non-linear registrations to remove the distortion from the b0.
  • Some possible tools include ANTS , DTI-TK, or BrainSuite.
  • The deformation fields from the warping should then be applied to all volumes in the DWI.

Example usage:

     enigma_epi_correct_commandLine.sh b0.nii.gz t1_to_b0.nii.gz dwi.nii.gz output_folder output_name