For some unknown reason, I am getting a residual plot written with each Eddy_Cuda run despite the --residuals flag not being set. I am running the following script and can't figure out why it keeps writing the residuals file. Any suggestions?
On a related note, the scripts I was initially provided have the --sep off moves flag included. I can't find any literature that tells me what if anything this flag does.
eddy_cuda --imain=${subjdir}/AP_PA --mask=${subjdir}/nodif_brain_mask --index=${subjdir}/index.txt --acqp=${subjdir}/acqparams.txt --bvecs=${subjdir}/bvecs --bvals=${subjdir}/bvals --fwhm=0 --topup=${subjdir}/topup_AP_PA_b0 --out=${subjdir}/eddy_unwarped --flm=quadratic --sep_offs_move --cnr_maps --repol --nvoxhp=2000 --ff=10
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