Hi!
I am trying to do TBSS on a population of MS-patients. My DTI images are distortion corrected during scanning and therefore I assume topup is not necessary. However, if I skip topup, then I am missing an output that's needed for the next step, eddy correction (using "eddy" command). Anyone that can recommend a solution for this? Should I just use eddy_cuda? "eddy_correct" could be an alternative but I've read that it should be avoided.
Hi Bianca,
This would be a great question to post in our new free medical imaging question and answer forum ( www.imagingQA.com ), there are already a few DTI /TBSS / FSL questions on there and experts in the community. If useful, please feel free to open a new topic at the link below :
https://community.imagingqa.com/c/questions/5
Hi Bianka,
the topup-output is optional for eddy, so you can leave that option off.
As the user guide states:
"--topup
This should only be specified if you have previously run topup on your data and should be the same name that you gave as an argument to the --out parameter when you ran topup."
Best,
Martin
Thank you very much for your helpful answers!
James O'Callaghan - I’ve posted the question according to your recommendation.
Martin Domin - thank you, I understand. But do I need to do eddy correction whatsoever if the data is already eddy corrected at the scanner?
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