Hi there,

I'm experiencing some problem with regarding the registration between the fiber tractography (made with TrackVis) and acpc aligned 3D (made with AFNI).
I described such an issue on the following MedIC post:

[medic.rad.jhu.edu]

In there, the acpc alignment was performed with Mipav software package. Suspecting it was a Mipav re-orientation fault during volume saving, I modified the first step performing the 3D acpc alignment with AFNI and saving it with 3dAFNItoNIFTI. Well, what I got was the same result described in the remaining steps, i.e. subsequent B0 to anat+acpc registration made by FSL-FLIRT shows a 180° rotation of the B0 with respect to the original 3D. Such a behaviour brings to an erroneous overlay between the tractography and the anat+acpc volume.

Is anyone able to explain why, to perform acpc alignment, both software (AFNI and Mipav) cause a 180° rotation of the original 3D volume, subsequently detected by FSL-FLIRT registration tool?
Acpc alignment should be a slight roto-translation of the volume, isn't? So why a rotational component of the registration matrix close to M = (-1 0 0; 0 -1 0; 0 0 1)?
So far I tried to make my own data processing "protocol" to process anatomical and DWI data to get fiber tractography on a acpc aligned volume. But it seems not to work. Is anyone able to show me an alternative BUT working procedure to perform such processing?

Thanks in advance for your help.