Topup on fsl v6 is much slower than fsl v5

Hello. We are having a runtime issue with FSLv6 topup and I am hoping someone could help us out…

On FSLv5, topup was working fine but we had to upgrade to FSLv6 so that we can run eddy_cuda9. On FSLv6, topup is taking forever to run (4.5 hours on v5 v.s. 18.5 hours on v6), and according to my benchmark, runtime for topup on FSLv6 seems to be growing exponentially with respect to the number of input slices. It seems to be pretty linear for FSLv5.


I am not sure what changes between fsl5 and fsl6 (I only see a few bug fixes in WhatsNew - FslWiki), but is this an expected outcome? Has anyone else seen a similar issue?

We’ve been stuck on this issue for weeks now, and I’d appreciate any help!

Maybe you can post your question in the FSL mailing list.