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Hi, either there's a problem with your data (make sure you're running BET on the B=0 image and not the 4D directions data) or in your bvecs or bvals. Cheers. On 24 May 2007, at 01:17, David Kideckel wrote: > hi. thank you for your support. once i run bet from the command > line (using cygwin), it does not seem to be working properly. but > when i use the gui, it does... > anyway, i am trying to rum dtifit from the command line and get the > following message: > 0 256 0 256 0 50 > 0 slices processed > Aborted <core dumped> > > Any idea why this is happening? Did I enter something wrong? > > Thanks. > David > > On 5/23/07, Tim Behrens <[log in to unmask]> wrote: > If you select dtifit from the drop down menu on the same page, all` > the information about file specifications is there. Don't forget to > end your bvecs and bvals files with carriage returns. > > Cheers > > T > > On 23 May 2007, at 18:53, David Kideckel wrote: > >> Hi. That was one of the firs things I did do. I will try to be >> more specific with my question. I want to do TBSS, and no >> tractography. So, would I do the following in this order: >> Eddy Correct >> BET >> DTI Fit >> >> If so, where is it in the manual specified how to create and input >> the bvecs and bvals files? I follow the link it gives in the FAQ >> section, but I can't seem to find this info. >> >> Thanks again for your help. >> David >> >> On 5/23/07, Tim Behrens < [log in to unmask]> wrote: >> Hi - if you go to >> http://www.fmrib.ox.ac.uk/fsl/fdt/index.html >> >> and select "processing pipeline", all should be clear. >> >> T >> >> On 23 May 2007, at 17:22, David Kideckel wrote: >> >>> Hi. Thank you for your response. Can you please send me this >>> information. I can't seem to find it on the FSL website. >>> Thanks you. >>> David >>> >>> On 5/23/07, Steve Smith < [log in to unmask]> wrote: Hi, >>> >>> Indeed - you should run eddy_correct and then bet and then dtifit to >>> produce the FA image - see the FDT manual pages for more details. >>> Sorry the TBSS page isn't clearer about that - we'll fix that >>> shortly. >>> >>> Cheers. >>> >>> >>> >>> On 22 May 2007, at 18:51, David Kideckel wrote: >>> >>> > Dear FSLers, >>> > >>> > I am new to TBSS and am wondering what the preprocessing steps are >>> > to do prior to TBSS. This information seems to be different on the >>> > FAQ section of the FSL website and the technical report on TBSS. >>> > >>> > Is it correct to assume that to compare 2 groups with diffusion >>> > data, I would need to run: >>> > Eddy correct >>> > Registration >>> > DTIFit >>> > TBSS >>> > >>> > I am unclear as to whether I need to run BET (brain extraction >>> > tool) and/or BEDPOST. >>> > >>> > Any guidance would be much appreciated. >>> > >>> > David Kideckel, PhD Candidate >>> >>> >>> -------------------------------------------------------------------- >>> ---- >>> --- >>> 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] http://www.fmrib.ox.ac.uk/~steve >>> -------------------------------------------------------------------- >>> ---- >>> --- >>> >> >> > > ------------------------------------------------------------------------ --- 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] http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---