Hello all,
In running probtrackx, we find that that the generated paths are not in the
correct orientation. Our input data consists of a preprocessed dataset
(using both AFNI and FSL tools) that is in nifti format. In order for the
dataset to be correctly oriented and to appear accurately in the viewer we
ran the following commands before running bedpostx:
fslorient -swaporient data.nii.gz
fslswapdim data.nii.gz x -y z data.nii.gz
As the resulting fiber paths from probtrackx were incorrectly oriented, the
commands above were applied to the fdt.paths file, but still did not result
in a correct overlay. We are wondering what the issue is here. Does the
bvecs file need to be adjusted to account for the changes in orientation
that were applied to to the diffusion dataset? Your assistance is much
appreciated.
best,
Sunita
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