Dear Marek,
> I would like to ask a general question about FSL, one specific about eddy_correction and the one about new eddy script.
> The general question:
> I have a data set of 1 b0 volume and 15 diffusion weighted volumes (DWI) of human spinal cord. Which scripts are suitable to use on this data set (I mean which are applicable to general data and which are applicable specifically only to brain? E.g. BET works obviously on brain only...)?
most of the diffusion tools can be used also outside the brain. eddy_correct, eddy, dtifit, bedpost etc should all work fine. Many of them take masks that you will have to make manually (because bet won’t work).
> Eddy_correct:
> I used eddy_correct on my data set and generally it works right but after application on same data random DWI volumes are all-zero (without any error massage) which produce wrong FA image. I use same magnet, same protocol, same everything, but sometimes eddy_correct works wrong and I do not know why. Can you help me?
> Eddy:
> You gave an example on FSL web site on data set with 5 b0 and 59 DWI images but it is possible to use eddy to my data set (1 b0 and 15 DWI images)? Could eddy gives better results than eddy_correct script? I mean if eddy can fix the problem with zero volumes which eddy_correct makes.
I suspect that 15 dwi might be pushing it a bit for eddy, but there is no harm in trying.
The problem with all zero sounds strange though. Have you looked at the resulting .mat files to see if you have some very large translations that have translated the object outside the FOV?
Jesper
> Thanks
> Marek
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