Hi Graham – Have you tried mri_convert? The 6.0 version should be able to extract diffusion gradient tables and b-value tables from most standard recent dicoms.

a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Warner, Graham Cary" <GWARNER@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, February 8, 2017 at 10:01 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] dcm2niix

Hi all,

Can we get dcm2niix added to the system instance of fsl? It can't find it in 5.0.7 or 5.0.9 (please let me know if it is somewhere else and I'm just not seeing it). I'm having problems generating .bval and .bvec files from certain DTI datasets using dcm2nii and the NITRC guys told me I should be using dcm2niix.

Thanks,
Graham