Hi Barbara:
1. The rotation component of the registration matrix from eddy_correct is
extracted for each DWI and applied to the corresponding gradient
vector.
2. dmri_pathstats is not a script, it's a C++ executable, so to edit it
you have to download the source code, modify, and recompile.
Alternatively, you can get the x, y, z coordinates of each voxel from
the pathstats.byvoxel.txt file and get values at that voxel with
something like: mri_info --voxel x y z dmri/dtifit_L3.nii.gz
a.y
On Fri, 17 Oct 2014, Barbara Kreilkamp wrote:
> Dear all,
> Do you have suggestions/ideas for me please?
> Thank you,
> Barbara
>
>
> -------- Original Message --------
> Subject:
> TRACULA preprocessing: bvector rotation, negative eigenvalues
> Date:
> Tue, 07 Oct 2014 19:09:00 +0100
> From:
> Barbara Kreilkamp <bakk....@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
>
>
>
>
>
>
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