As noted in the email, Ill reply with the most simple for now:
Yes, the default is to calculate the streamline counts. To calculate the
mean FA over the structural connection, should be to add the following arguments to
-scale_file yourfaimage.nii -stat_edge mean
As noted in email correspondence, the
apparent fiber density is a bit more tricky, as the heuristic (http://mrtrix.readthedocs.io/en/latest/reference/commands/afdconnectivity.html) here is dependent on:
- All images are required to be intensity normalized
- Sum of FOD amplitudes are corrected by the streamline length, and
- Either calculated for fixel with greatest density of streamlines, or all fixel voxels (i.e.
The issue is that perhaps your subject’s parcellation is in native space? And hence you would need to co-register your image into MNI space.
With that being said, I would first check the strides of your parcellation image?