I will add that you can run the HCP pipelines with the latest version of FSL. The question Tim was responding to was how to get exactly what was run within ConnectomeDB.
Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Timothy B. Brown" <[email protected]<mailto:[email protected]>> Organization: Washington University in St. Louis Date: Wednesday, March 1, 2017 at 3:29 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] HCP Pipelines v3.19.0 pre-reqs? Hi Michael, Unfortunately, the situation gets a little "messy". The prerequisites for v3.19.0 are (for the most part) the same as those for v3.4.0. However, due to a change that was introduced in FSL at version 5.0.7 that is not backward compatible, there are some specific pipelines that require different versions of FSL. For the most part, FSL 5.0.6 is required to get results that are compatible with the HCP results. But for the diffusion preprocessing pipeline, you will need FSL version 5.0.9. In fact, we actually used a version of the eddy program that is to be included in 5.0.10 (which I do not believe is officially released just yet.) See the message here (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;5ade7210.1611) for some information on how to create a "patched" version of 5.0.9 that contains the 5.0.10 version of the eddy program. For the ReApplyFix pipeline, you will also need version 5.0.9. (Since it does not use the eddy program, it does not matter if this is the actually released v5.0.9 or one that is "patched" to include the 5.0.10 version of eddy.) Since the DeDriftAndResample pipeline invokes the ReApplyFix pipeline, it requires FSL version 5.0.9. I have tried to include specific version checks and warnings in any pipelines that specifically require v5.0.9 or above. I am in the process of trying to get or verify that all the pipelines in entire product can use the same version of FSL (v5.0.9+), but I had to maintain some of them in the FSL v5.0.6 state to make sure all our HCP data was processed the same way. Wish I had a simpler answer for you, Tim On 03/01/2017 02:40 PM, Michael Stauffer wrote: Hi, I'm installing v3.19 of the HCP Pipelines for a user on my system. Are the pre-reqs the same for 3.4.0 that I already have installed? The documentation points to the 3.4.0 release notes. Thanks -M _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Timothy B. Brown Business & Technology Application Analyst III Pipeline Developer (Human Connectome Project) tbbrown(at)wustl.edu ________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
