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Dear Saad, Thanks u very much - I will do some more tests and will get back to u with the results. Rotem Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel 2014-08-13 15:31 GMT+03:00 Saad Jbabdi <[log in to unmask]>: > Hi > I don’t have any experience with MRIconvert. We use dcm2nii (part of > MRIcron). But Michael is right in that you need the gradient orientations > to be relative to the imaging box. > It is difficult to tell from your snapshot whether there is something > wrong with your DTIFIT (apart from the fact that you have very coarse > through-plane resolution, but this hasn’t got anything to do with rotating > the bvecs). > > Cheers > Saad > > > On 12 Aug 2014, at 07:02, Rotem Saar <[log in to unmask]> wrote: > > > > > Dear FSL experts, > > I'm currently trying to analyze Diffusion data in FSL. I'm working with > dicoms from a 3T Philips scanner, 33 directions*60 slices, Bvalue = 800. > I used MRIconvert and transformed the dicoms into FSL-NIFTI format. It > created all the necessary files. > At the first step, I'm interested in extracting the FA & MD maps. > The thing is - when I look at the gradient matrix created using MATLAB > script that reads the directions from the dicom header - I get one table, > but the bvecs file created in MRIconvert looks different. > Michael told me that FSL is expecting the rotated matrix as input, but > when I did it - I got this map (I am not able to attach it to this email so > I added a link): > http://tinypic.com/r/skzwqa/8 > I think that something is wrong but can't specify what. > I will really appreciate your help, > > Thanks ! > > > ------------------------------------------------------------------ > Saad Jbabdi, PhD > MRC Career Development Fellow & > University Research Lecturer > > FMRIB Centre, University of Oxford, > John Radcliffe Hospital, Oxford, OX3 9DU, UK. > tel (+44)1865-222466 (fax 717) > www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi > > > >