PROBLEM: FSL eddy removes vertex of brain

PROBLEM: Eddy removes half slices (either Right or Left sides) of the vertex brain in the most superior or the lowest inferior slice of the brain (when viewed in axial format).


I am running FSL Eddy without topup (as I only have single fixed phase encoding with one b0 image at thE beginning of my diffusion sequence) on my scans- AP phase encoded single shell b = 1000, 65 direction diffusion data. I have performed the following steps:

  1. Mrtrix DWIDenoise.

  2. MRtrix degibbs.

  3. fslroi to extract b0 volume.

  4. bet to to generate brain mask from b0 volume.

  5. eddy --imain=DENOISED_DEGIBBED_DATA --mask=B0BRAINMASK --acqp=acqparams.txt --index=index.txt --bvecs=DEBNOISED_DEGIBBED.bvec --bvals=DENOISED_DEGIBBED.bval --out=eddy_corrected

I am unable to get the readout time or to calculate it from the dicom headers (the headers are incomplete as it is a GE scanner) so I have set the 4th column in acqparams.txt as 0.05.

Does anyone know why this is happening and what the solution is? I suspect I may need to pad the image superiorly and inferiorly or change the interpolation method?

Many thanks