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 checked if the extracted bvecs are correct.

To check if the extracted bvecs are correct, I used Diffusion Toolkit together with the extracted bvecs to do deterministic tractography. Then I checked the shape of the extracted nerve fibers. I have put a slide deck in the following dropbox folder showing that the shape of the extracted nerve fibers don’t look right:

https://www.dropbox.com/s/1bt6on0rwm9url6/x_inversion.pptx?dl=0 https://www.dropbox.com/s/1bt6on0rwm9url6/x_inversion.pptx?dl=0

Then I inverted the x-components of the extracted bvecs, and did the tractography again. This corrected the shape of the extracted nerve fibers (see the slide deck).

I additionally had a look at the extracted dtift_V1 vectors under the two conditions, i.e. before and after x-component inversion. The results showed the same thing: x inversion corrects the images.

I just wanted to see if others have had the same problem and confirm that I should invert the x-component of the bvecs extracted via mri_convert (I had the same experience with dcm2nii tool, where I had to invert the z-component of the extracted bvecs).

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 mailto:emad@nmr.mgh.harvard.edu