Dear FSL team,
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?
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
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