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Not here: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ But yes here: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslOverview And here: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/WhatsNew Just mildly confusing.... Stefano Marenco, MD NIMH/CBDB 10 Center Drive, Bldg 10 room 3C103 Bethesda MD 20892 Tel 301 435-8964 Fax 301 480-7795 Email: [log in to unmask] From: Stephen Smith [mailto:[log in to unmask]] Sent: Wednesday, September 26, 2012 10:15 AM To: [log in to unmask] Subject: Re: [FSL] TopUp --datain Yes they are! (the joy of wiki :-) On 26 Sep 2012, at 15:09, Marenco, Stefano (NIH/NIMH) [E] wrote: I see now, it just is not listed in the main tools, thanks! Stefano Marenco, MD NIMH/CBDB 10 Center Drive, Bldg 10 room 3C103 Bethesda MD 20892 Tel 301 435-8964 Fax 301 480-7795 Email: [log in to unmask]<mailto:[log in to unmask]> -----Original Message----- From: Jesper Andersson [mailto:[log in to unmask]]<mailto:[mailto:[log in to unmask]]> Sent: Wednesday, September 26, 2012 10:04 AM To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] TopUp --datain Hi there, topup is now openly supported. If you go to what's new in FSL 5 you'll find links to the documentation (maybe that's what you did?). Jesper On 26 Sep 2012, at 16:01, Marenco, Stefano (NIH/NIMH) [E] wrote: Is topup now part of the official distribution? I could not find it among the main list of tools, although when I search for topup I can find a Users guide and an example. Is this now openly supported or still in testing? Stefano Marenco, MD NIMH/CBDB 10 Center Drive, Bldg 10 room 3C103 Bethesda MD 20892 Tel 301 435-8964 Fax 301 480-7795 Email: [log in to unmask]<mailto:[log in to unmask]> -----Original Message----- From: Jesper Andersson [mailto:[log in to unmask]]<mailto:[mailto:[log in to unmask]]> Sent: Wednesday, September 26, 2012 3:58 AM To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] TopUp --datain Hi Michel, as a little addendum to Saads reply I should stress that topup can only be used if the data was acquired in a way that allows it. I.e. if data was for example acquired twice with opposing phase-encode blips. Data that was acquired without planning to use topup is unlikely to be possible to process with topup. This is equivalent to other types of distortion correction where if for example one has not acquired fieldmaps one cannot use fieldmap based corrections. Good luck Jesper On 26 Sep 2012, at 09:49, Michel Thiebaut de Schotten wrote: Dear experts, This morning I tried to run topup for the first time, to correct distortion on a DWI dataset. Following the help menu I wrote the following command topup --imain=DWI.nii --datain=bvecs But the following error occurred: TopupFileIO:: msg=TopupDatafileReader:: error reading file bvecs What is supposed to be the --datain if not the Bvec? Thanks for your help an the new release of FSL, Kind regards, Michel --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------