Dear Jesper,
Thanks a lot for your quick reply! I followed your advice and set the negative values after eddy current correction to 0.0001. Interestingly, this improves the hyperintense, noisy voxels at the edges of the brain. However the hyperintense voxels within the brain so far seem to be unaffacted by this. The FA-maps therefore still look quite noisy.
Concerning the eddy current correction, we have always used the eddy_openmp command (we do not have a CUDA-gpu), which, as far as I understood, corresponds to the "newer" eddy command. On the other hand, we have also used topup in our previous datasets, so I guess the interpolations done within topup also smooth the images usually? As we unfortunately cannot use topup this time (all b0-volumes have been acquired in the same direction), do you think it might be advisable to use eddy_correct for this dataset instead of the new eddy command in order to decrease the noise?
Again thanks for your support!
Best,
Theodor
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