Hi Emad - I wouldn't do tractography to check the gradient vectors. All you need is to look at are the principal eigenvectors of the tensors (dmri/dtifit_V1.nii.gz), displayed as lines (not just RGB map, that's less informative). If, for example, the z coordinates need to be inverted, then the eigenvectors will look wrong in the coronal and sagittal view (the two views that involve the z dimension).
Hope this helps, a.y
On Mon, 4 Jan 2016, Emad Ahmadi wrote:
Hi FreeSurfer Experts,
Happy New Year!
I am using mri_convert to extract b vectors (bvecs) from diffusion images obtained at Bay 4. Then I use TRACULA for reconstructing white-matter pathways. The shape of the reconstructed pathways are odd, so I wanted to check if the extracted bvecs are correct.
To check if the extracted bvecs are correct, I put them in Diffusion Toolkit, did deterministic tractography, and checked the shape of the extracted nerve fibers. In the attached ppt file, the first three slides show the shape of the extracted fibers. You can see that they don’t look right.
Then I inverted the X components of the extracted bvecs, and did the tractography again. The last three slides show the result, which look right now.
I had the same experience with dcm2nii tool, where I had to invert the Z component of the extracted bvecs. Just wanted to see if others have hit the same problem and confirm that I should invert the X component of the bvecs extracted via mri_convert.
I hope a wonderful new year for everyone! Emad
Emad Ahmadi, MD
Research Fellow in Radiology Massachusetts General Hospital Harvard Medical School
25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad@nmr.mgh.harvard.edu