-------- Original Message --------

Subject:	TRACULA preprocessing: bvector rotation, negative eigenvalues
Date:	Tue, 07 Oct 2014 19:09:00 +0100
From:	Barbara Kreilkamp <bakk.hbg@gmail.com>
To:	Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

Dear Freesurfers,

I am looking for information on how exactly the b-table gets rotated.

1. It seems that eddy_correct runs once with 12 doF, and then the 
bmatrix gets updated based on this registration. Would you please confirm?

2. I know that my data has negative eigenvalues (most of them seem to 
appear in the 'halo' around the images), and I would like to save L2, L3 
voxel values within tracts in the pathstats.byvoxel.txt file. How may I 
edit dmri_pathstats to accommodate this? My aim is to identify MD, RD, 
FA, AD (L1) voxel values that were biased by a lot of noise.

Thank you very much,
Best,
Barbara