Dear Georg,
>
> I am working on a DWI data set (n=20; 64 directions; one b0; b=3000; PE dir=A>>P; Echo spacing=0.82ms; EPI factor=128) and currently I'm trying to preprocess this data for later tractography analysis.
>
> Unfortunately there were no b0's with reversed phase-encoding collected for the data set, so I can't run topup (I have field maps however, so considering epi_reg later).
> I have used eddy_correct and processed the data successfully, however now I want to use the new(er) EDDY to preprocess and then compare to the output to eddy_correct (are these expected to be significantly different?).
I would expect them to be different.
>
> When I run EDDY I use the following command:
>
> eddy --imain=rawdata.nii --mask=rawnodif_brain_mask.nii --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals --flm=quadratic --niter=5 --verbose --out=EDDY_corrected_rawdata.nii
>
> My parameter files are:
>
> acqparams.txt
>
> 0 -1 0 0.104
>
> index.txt
>
> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
>
> I don't get any errors when I run EDDY, but the output 4D is (visually) not any different from my input raw data file; whereas i.e. the output of eddy_correct is clearly different from the raw data.
> What am I doing wrong?
it is hard from this description to know what is going on. Maybe you can run it again, this time removing .nii from the —out parameter and add —very_verbose? This would give you lots of debug information to the screen that you could maybe then cut-and-paste into an email to me?
Jesper
>
> Thank you for helping,
> Best,
>
> Georg
>
> Georg Kerbler
> Postdoctoral Research Fellow
> Brain and Action Laboratory
> Queensland Brain Institute
> University of Queensland
> Building 79 Upland Road, St Lucia QLD 4072
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