Dear freesurfer experts,

For diffusion analysis in freesurfer - I want to know which gradient matrix freesurfer expects.

The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for converting dicoms to nifti) looks different.

This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix.

So my question is which table should I use for diffusion analysis in freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ? 

Thanks