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Dear Thais, > > I did the FSL course last year (Oxford) and learned that to process the DTI images wee need to use 'topup' and 'eddy'. However, the dataset that I will analyse was collected quite while ago and as far as I know, it was not acquired with 2 different phase encoding directions, so I guess I cannot use 'topup' and 'eddy'. So, could you please help me with my queries. > > 1- In this case, instead of 'eddy' I will have to use 'eddy_correct' from the FDT. >>> Is this the way forward? Any alternatives? you need two PE directions to run topup. It is not necessary in order to run eddy. When you run eddy without having run topup first it means that you only correct for eddy current distortions and subject movement (i.e. not for susceptibility). But that is still likely to be better than to use eddy_correct (that doesn’t attempt to correct for susceptibility either). Can you please give me some details about your diffusion data set, such as number of diffusion directions, if directions were sampled on the whole or half sphere? Jesper > > 2- To 'eddy_correct', I do not need to use the 'fslroi' command to select a volume without diffusion weighting, as in 'eddy_correct' there is the 'reference no' which already accomplish for it. >>> Am I correct? > > 3- For the 'bet' command, which will create a file to use on 'dtifit', do we have to use 'fslroi' on the original DTA.nii file (to select a volume without diffusion weighting), or can we use 'bet' directly on the original DTA.nii file? > > Many thanks for your help! > > Regards, > > Thais Minett