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