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Dear Christina, > > I am currently working on processing my data with eddy. My data has only been collected in one direction (A>>P; 30 directions run twice, 2 B0s), so running topup is not appropriate in this case. Given I will not be using an output from topup for my mask, what should I use in its place? Would I just run BET and use the mask from that? yes, just run bet on the first b0. It is not at all critical, but if anything it is better that it is too small than too large. > > Also, I just want to confirm the command I would use for eddy: > > eddy --imain=data --mask=[mask from question above] --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals --out=eddy_corrected_data > > Acqp= 0 -1 0 .095 > > Index = Sixty-two 1s Yes, that looks like a good “basic” eddy call. Depending on what version of eddy you are running I would also recommend the --repol option (described here https://www.ncbi.nlm.nih.gov/pubmed/27393418). If you are working with a population that moves a lot (babies, children etc) I would also recommend taking a look at the slice-to-vol options (described here https://www.ncbi.nlm.nih.gov/pubmed/28284799), but that requires the latest eddy version and access to a GPU. Jesper > > Thanks in advance for your time! > Cristina > > ######################################################################## > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1