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Hi FSL DTI Experts, I am working with multishell DWI data and I am struggling with poor data CNRs. I am wondering whether I might be doing something wrong in my steps. I started off by doing TOPUP using the the pair of b0s from my first b0 scans (b = 300). Should I be doing the TOPUP on my b = 1000 / b = 2000 shells instead? My colleague told me that the b0s for TOPUP must be the first volume. 1) If I have collected the same number of volumes in my PA as my AP scans, should I do the eddy correction on the total merged volumes? I read somewhere on the mailing list that the person achieved higher CNR when he only used the eddy-corrected AP scans after TOPUP. For context, my data comes from people with movement disorders so there is a lot of movement compared to my healthy controls. The total number of volumes is 208. 104 for each AP and PA. Command when I use the merged AP and PA datasets.eddy_cuda8.0 --imain=merged_data.nii --mask=brainmask.nii --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bval --out=output --verbose --data_is_shelled --fwhm=0 --flm=quadratic --niter=8 --fwhm=10,6,4,2,0,0,0,0 --repol --ol_type=both --mporder=8 --s2v_niter=8 --estimate_move_by_susceptibility --cnr_maps --topup=topup --json=ap.json --verbose Command when I use the merged AP and PA datasets.eddy_cuda8.0 --imain=ap.nii --mask=brainmask.nii --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bval --out=output --verbose --data_is_shelled --fwhm=0 --flm=quadratic --niter=8 --fwhm=10,6,4,2,0,0,0,0 --repol --ol_type=both --mporder=8 --s2v_niter=8 --estimate_move_by_susceptibility --cnr_maps --topup=topup --json=ap.json --verbose 2) After running eddy_quad, the averaged CNR across the 3 shells were mostly in the range of 0.8-1.0, and much lower in the patient groups. Is this considered very bad? I read the very nice Eddy Quad paper in Neuroimage Clinical and the CNR reported was around 1.5 and higher. 3) Is there anything else I could do improve the quality of the data? Thanks for your patience. Best Regards,Shane ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1