Dear Maxim,
> it seems that after eddy_correct my data.nii and
> nodif_brain_mask.nii have
> different dimensions. fslview wont't load them together, and spm
> checkreg
> shows them completly spatialy unregistered. is that normal- -or
> might this
> be the problem for strange FA maps after dti fit ?
I had a look at your data before and after eddy_correction, and it
hasn't worked very well. I have a feeling that you left 0 as reference
volume. I tried using 1 instead, the diffusion weighted volume, and
the results look much better. I then used bet (with -f 0.3) to
generate a brain mask and fit it all into dtfit. There is one slice
with some problems (you should look through the individual dwi's for
that slice), but on the whole a very nice looking FA map.
Good Luck Jesper
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