I am setting a pipeline to preprocess DWI data and it seems there are no tools inside DTIPrep to correct for field inhomogeneities. I have seen previous reports using AFNI or FSL that try to correct field inhomogeneities by registering b0 image with a standard T2 image or by calculating a kind of field map (topup procedure in FSL). Is there a similar tool in DTIPrep?

Thanks,
I do appreciate any comments.

Hi Daniel,

If you are interested in preprocessing your data using FSL’s topup to correct for these artifacts prior to running dtiprep, I am happy to offer guidance for doing that. In my experience working with dtiprep, we have first run tools from fsl for preparing the data (correcting field in homogeneities) prior to dtiprep.

Thanks Rachel,

  Unfortunately, I do not have PA and AP images from my acquisition to run topup. I just was wandering if there was any procedure in DTIPrep or Slice to run an equivalent procedure, such as warping b0 image to T2 images and then apply the wrap field to the DWI as other groups have done using ANTS.
 Otherwise, I guess I can always run this procedure before or after DTIPrep (always before computing the tensors).

Thanks.