Dear Amanda,
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> I am new to DTI data analysis and was looking for some input on what commands I should be using to process my DTI data.
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> The data are kind of old and simply consist of one scan, 58 volumes including three B0 images in the beginning (all acquired A>>P). I also have a magnitude field map and a phase field map.
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> I know that I cannot use topup, but should I still use eddy rather than eddy_correct? If so, would I apply the preprocessed fieldmap to the eddy output with fugue?
eddy is considerably better than eddy_correct for almost any data set, so you should use that. For the fieldmap you have two options. One is, as you suggest, to apply fugue to the eddy corrected data set. The other is to do all the pre-processing to the fieldmap (prelude etc) so that you get a fieldmap in Hz, register that fieldmap to the first volume of your diffusion data and then pass that to eddy using the --field option.
If you use the latter option it is crucial that you get the readout time in the --acqp file correct.
Jesper
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> The end-goal is just to run standard TBSS analysis if that provides any context.
>
> Any advice is appreciated.
> Amanda
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