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).
CODE WHICH PRODUCES PROBLEM:
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:
fslroi to extract b0 volume.
bet to to generate brain mask from b0 volume.
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?