Hello,
I have a question regarding MRtrix3 gradient table(x y z b). I use MRtrix in Connectome Mapper. I created a table with the format which is mentioned on the MRtrix website.my table is here. Is this table wrong? My tractography result with this table is not nice. Please help me to find the correct format. Thank you.
0.00000 0.00000 0.00000 0
-0.00000 1.00000 0.00000 1000
1.00000 0.00000 0.00000 1000
-0.00000 0.00000 1.00000 1000
0.52573 0.00000 -0.85065 1000
-0.52573 0.00000 -0.85065 1000
0.85065 0.52573 0.00000 1000
-0.00000 -0.85065 0.52573 1000
-0.00000 -0.85065 -0.52573 1000
-0.80902 0.30902 -0.50000 1000
0.80902 0.30902 -0.50000 1000
-0.80902 -0.30902 -0.50000 1000
-0.80902 0.30902 0.50000 1000
0.30902 -0.50000 0.80902 1000
-0.30902 0.50000 0.80902 1000
0.30902 0.50000 -0.80902 1000
0.30902 0.50000 0.80902 1000
0.50000 -0.80902 0.30902 1000
-0.50000 0.80902 0.30902 1000
0.50000 0.80902 0.30902 1000
0.50000 0.80902 -0.30902 1000
-0.50000 -0.80902 -0.30902 1000
That looks fine to me. What is the problem exactly? What commands are you using that involve this table, and what is the error message?
You can check whether your gradient table is oriented correctly using the dwigradcheck command, as per https://www.ncbi.nlm.nih.gov/pubmed/24968247 by simply running:
dwigradcheck dwi.mif -mask brainmask.mif
Cheers,
Ben
Thank you for the response. When I use this gradient table in deterministic tractography with DTK, tractography image is nice, but MRtrix probabilistic tractography image is not good.
Please advise me to fix this issue.
OK, I’m not sure there is anything to fix here - hard to tell from such a sparse tractogram. Bear in mind that probabilistic streamlines will always be much messier than deterministic streamlines, and you need to produce many more streamlines than you might otherwise be used to to get a decent representation of what’s going on. Try seeding at least 100,000 streamlines to get a better idea of the connections.
Thank you very much. This helps a lot!
Thank you very much for the reply.
