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: e...@nmr.mgh.harvard.edu <mailto:e...@nmr.mgh.harvard.edu>
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