Hello,
I did all of my DTI preprocessing through tracula. I now am using FSL probtractx (which utilizes the bedpost stage output) to explore pathways from the amygdala to the ventromedial prefontal cortex.
When I used FSL's probtractx, when I viewed the tract. The tract was in the wrong area of the brain.
So, I think this may have something to do with the transfromation matrices I gave it via tracula.
*FSL asks for the seed to diffusion transformation matrix so that it can convert your seed masks from MNI space to diffusion space. I gave the transformation matrix in the dmri folder under xfms, titled mni2diff.bbr.mat. I have a feeling this may be the issue.
* I then tried to use the FLIRT registration tool through FSL to get the appropriate transformation matrices. It asks for the bedpost directory. I got an error saying it could not read my no_dif_brain_mask.nii.
I am not sure what transformation matrix to give and was wondering if you could give me some guidance.
Thanks,
Emily