Re: [HCP-Users] Processing Diffusion MRI Data

[Glasser, Matthew]

Months but hopefully not a large number.  We’re just double checking that the database pipeline works right and then the jobs will be kicked off.  Then the results will need to be packaged up and put on the website.   Peace, Matt. From: Matthew George Liptrot <matthew.lipt...@di.ku.dk> Date: Wednesday, February 18, 2015 at 9:10 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Processing Diffusion MRI Data Hi Stam, This release of the bedpostx results sounds great! Any idea of a timeline (days or months)?  I’m just trying to gauge whether we should start the cluster off doing the calculations ourselves or wait for the release… Cheers, M@ --  Matthew George Liptrot Department of Computer Science University of Copenhagen &  Section for Cognitive Systems Department of Applied Mathematics and Computer Science Technical University of Denmark http://about.me/matthewliptrot On 16/2/15 18:48 , "Stamatios Sotiropoulos" <stamatios.sotiropou...@ndcn.ox.ac.uk> wrote: Hi Derek Please notice that model=3 is not officially released yet in FSL. Also, there should be a future HCP release in the near future including bedpostx results, with the optimal parameters. Stam On 16 Feb 2015, at 16:25, Archer,Derek B <arche...@ad.ufl.edu> wrote: Matt, Thanks for the fast reply.  I will use these three inputs in bedpostX.    Derek   From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]  Sent: Monday, February 16, 2015 11:24 AM To: Archer,Derek B; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Processing Diffusion MRI Data   Why do you need to use FLIRT/FNIRT with already registered data?  As for the others and aside from the flags you already mention, I think the recommendation for bedpostX will include these flags:   -n 3 (for 3 fibers)  --cnonlinear --rician --model=3   Not all of this may yet be available in the public release (you might need to use --model=2 for now).   Peace,   Matt.   From: <Archer>, Derek B <arche...@ad.ufl.edu> Date: Monday, February 16, 2015 at 9:16 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Processing Diffusion MRI Data   Hello,   I am trying to analyze the preprocessed diffusion data, however, I am having some difficulties. Is there some documentation that I could look at that outlines how to use bedpostx, FLIRT/FNIRT, DTIFIT and probtrackx with this data?   From what I’ve found in the archives, I need to do the following:   Bedpostx:  include the –g option FLIRT/FNIRT:  do I include any extra options here? DTIFIT:  include the –gradnonlin option   Is this all that needs to be done to have this data ready for tractography? Or are there steps that I have missed?   Please let me know if there is any documentation I have failed to locate.    Thanks, Derek Archer       _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users