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Hi Isobel, they need to have the names: "bvecs" and "bvals" so you need to rename them. Moises. On 5 January 2015 at 02:33, Isobel French <[log in to unmask]> wrote: > Hi Moises, > > Yes I do have those files, as attached below: > > > PS_s006a1001.bval > <https://docs.google.com/file/d/0BzDE7mjXpVELSERvMG4zU2d2Ulk/edit?usp=drive_web> > > PS_s006a1001.bvec > <https://docs.google.com/file/d/0BzDE7mjXpVELWjc5OFFEYlJmTzA/edit?usp=drive_web> > > Is there a problem with the way that files are named? > > I see. Thanks for your guidance. > > > *Best regards,* > > *Isobel French* > > *Academic Coordinator and Research Officer* > *Neurosurgery Research Unit, Division of Neurosurgery* > *Department of Surgery, Faculty of Medicine* > *Suite 15 T8-4a * > *Level 4, Menara Timur* > *University of Malaya Medical CenterDivision of Neurosurgery* > *016-7937605* > *03-79493138* > > On Fri, Jan 2, 2015 at 10:43 PM, Moises Hernandez <[log in to unmask]> > wrote: > >> Hi Isobel, >> >> bedpostx needs a file called "bvecs" (An ASCII text file containing a >> list of gradient directions applied during diffusion weighted volumes) and >> a file called "bvals" (list of bvalues applied during each volume >> acquisition). >> >> Do you have these files in the directory /Users/neuro/Desktop/PS/ >> Tensor32directionsPS/bedpostX_PS ? >> >> Also, you are not passing the parameters correctly. If you are going to >> use the default options you just need to type: >> >> *bedpostx bedpostX_PS* >> If for example, you want to estimate a different number of fibres >> (default is 2) you can type: >> *bedpostx bedpostX_PS -n 3* >> >> i.e. after any parameter, you need to specify a value. For instance: >> *bedpostx bedpostX_PS -n 3 -model 2 -b 3000* >> >> Moises. >> >> On 2 January 2015 at 08:08, Isobel French <[log in to unmask]> wrote: >> >>> Hi Moises, >>> >>> When I typed in the command line, this is the response I got: >>> >>> neuros-iMac-2:~/Desktop/PS/Tensor32directionsPS] neuro% bedpostx >>> bedpostX_PS -n-w-b-j-s-model >>> subjectdir is /Users/neuro/Desktop/PS/Tensor32directionsPS/bedpostX_PS >>> /Users/neuro/Desktop/PS/Tensor32directionsPS/bedpostX_PS/bvecs not found >>> [neuros-iMac-2:~/Desktop/PS/Tensor32directionsPS] neuro% >>> >>> Am I doing something wrong here with the command line or is it some >>> other issue? I did get a similar response when I ran dtifit n my data. >>> However thee were no issues when I inserted the data files manually. >>> >>> Thanks. >>> >>> >>> *Best regards,* >>> >>> *Isobel French* >>> >>> *Academic Coordinator and Research Officer* >>> *Neurosurgery Research Unit, Division of Neurosurgery* >>> *Department of Surgery, Faculty of Medicine* >>> *Suite 15 T8-4a * >>> *Level 4, Menara Timur* >>> *University of Malaya Medical CenterDivision of Neurosurgery* >>> *016-7937605* >>> *03-79493138* >>> >>> On Thu, Jan 1, 2015 at 2:12 AM, Moises Hernandez <[log in to unmask]> >>> wrote: >>> >>>> Hi Isobel, >>>> >>>> There are several versions of FSL 5.0. (5.0.1, 5.02, ... 5.0.8) >>>> Can you specify what version do you have ? >>>> >>>> It seems a problem in the GUI. >>>> Have you tried to run bedpostx using command line? >>>> >>>> here you can see how to do it: >>>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX >>>> >>>> in section: >>>> >>>> >>>> *Command line utility* >>>> Best, >>>> Moises >>>> >>>> >>>> >>>> >>>> On 31 December 2014 at 03:26, Isobel French <[log in to unmask]> >>>> wrote: >>>> >>>>> Hi Moises, >>>>> >>>>> I am usin FSL version 5.0 and yes I am able to open the files under >>>>> bedpostX with fslview. >>>>> No I do not have the directory /Users/neuro/Desktop/PS/ >>>>> Tensor32directionsPS/bedpostX_PS.bedpostX, >>>>> >>>>> Would you know what the problem is? >>>>> >>>>> Thanks. >>>>> >>>>> >>>>> *Best regards,* >>>>> >>>>> *Isobel French* >>>>> >>>>> *Academic Coordinator and Research Officer* >>>>> *Neurosurgery Research Unit, Division of Neurosurgery* >>>>> *Department of Surgery, Faculty of Medicine* >>>>> *Suite 15 T8-4a * >>>>> *Level 4, Menara Timur* >>>>> *University of Malaya Medical CenterDivision of Neurosurgery* >>>>> *016-7937605* >>>>> *03-79493138* >>>>> >>>>> On Wed, Dec 24, 2014 at 6:12 PM, Moises Hernandez <[log in to unmask] >>>>> > wrote: >>>>> >>>>>> Hi Isobel, >>>>>> >>>>>> what version of FSL are you using ? >>>>>> >>>>>> Can you open your data, >>>>>> /Users/neuro/Desktop/PS/Tensor32directionsPS/bedpostX_PS with fslview ? >>>>>> >>>>>> Do you have this directory: /Users/neuro/Desktop/PS/ >>>>>> Tensor32directionsPS/bedpostX_PS.bedpostX ? >>>>>> >>>>>> Best, >>>>>> Moises. >>>>>> >>>>>> On 24 December 2014 at 03:03, Isobel French <[log in to unmask]> >>>>>> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I'm using OS X 10.8.5. No I am not using any other software for >>>>>>> this. Is it a problem with the system? Thanks. >>>>>>> >>>>>>> >>>>>>> *Best regards,* >>>>>>> >>>>>>> *Isobel French* >>>>>>> >>>>>>> *Academic Coordinator and Research Officer* >>>>>>> *Neurosurgery Research Unit, Division of Neurosurgery* >>>>>>> *Department of Surgery, Faculty of Medicine* >>>>>>> *Suite 15 T8-4a * >>>>>>> *Level 4, Menara Timur* >>>>>>> *University of Malaya Medical CenterDivision of Neurosurgery* >>>>>>> *016-7937605* >>>>>>> *03-79493138* >>>>>>> >>>>>>> On Wed, Dec 24, 2014 at 1:57 AM, Watson, Christopher < >>>>>>> [log in to unmask]> wrote: >>>>>>> >>>>>>>> What OS are you using? Are you also trying to use SGE or some other >>>>>>>> software for utilizing a cluster? >>>>>>>> >>>>>>>> ________________________________________ >>>>>>>> From: FSL - FMRIB's Software Library [[log in to unmask]] on >>>>>>>> behalf of Isobel French [[log in to unmask]] >>>>>>>> Sent: Monday, December 22, 2014 11:11 PM >>>>>>>> To: [log in to unmask] >>>>>>>> Subject: [FSL] BedpostX Problem >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> When I tried loading my data into bedpostX, a pop-up came up >>>>>>>> saying' child process exited abnormally', along with the output attached >>>>>>>> below: >>>>>>>> >>>>>>>> >>>>>>>> [ >>>>>>>> https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] >>>>>>>> bedpostcom_log.tcl< >>>>>>>> https://docs.google.com/file/d/0BzDE7mjXpVELTEZmWnYtNG00alk/edit?usp=drive_web >>>>>>>> > >>>>>>>> >>>>>>>> Do you all know what seems to be the problem? >>>>>>>> >>>>>>>> Thanks. >>>>>>>> >>>>>>>> Best regards, >>>>>>>> >>>>>>>> Isobel French >>>>>>>> >>>>>>>> Academic Coordinator and Research Officer >>>>>>>> Neurosurgery Research Unit, Division of Neurosurgery >>>>>>>> Department of Surgery, Faculty of Medicine >>>>>>>> Suite 15 T8-4a >>>>>>>> Level 4, Menara Timur >>>>>>>> University of Malaya Medical CenterDivision of Neurosurgery >>>>>>>> 016-7937605 >>>>>>>> 03-79493138 >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >