topup is not an alternative to eddy.
eddy and eddy_correct are alternatives for eddy current correction.
topup and fugue are alternatives for b0 induced distortion correction.
eddy is better than eddy_correct, but appreciates data acquired on the
whole sphere and with reversed phase encoding directions. Topup is better
than fugue for diffusion data, but requires data acquired with reversed
phase encoding directions (whereas fugue requires a field map).
It's always a good idea to use the best eddy current and b0 distortion
correction methods your data will support.
Peace,
Matt.
On 9/24/13 12:26 PM, "Joseph Orr" <[log in to unmask]> wrote:
>Topup is an alternative to eddy correction. Whether or not to use it
>depends on whether your data has reverse encoded scans:
>http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP/Faq
>
>Depending on how your data was collected you will need to run either eddy
>or topup
>
>-----Original Message-----
>From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>Behalf Of Diane Goldenberg
>Sent: Tuesday, September 24, 2013 11:04 AM
>To: [log in to unmask]
>Subject: [FSL] Tractography
>
>Hello,
>
>I'm interested in performing a tractography analysis in a network
>containing 10 ROIs by examining the tracks between ROI pairs. The ROIs
>are in MNI space. My question is, when is using Topup appropriate? If I
>register my ROIs to diffusion space and then perform the tractography
>analysis, is Topup necessary?
>
>Thank you,
>Diane
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