Hi Armin,
Here is a general plan of attack that might help…
FD, FC and FDC are fixel-based metrics, so implementing a single-tissue or multi-tissue FBA pipeline would be a good start.
Then try sh2peaks ${template_fod} Template_peaks.nii.gz , and feed Template_peaks.nii.gz as an input into TractSeg. This will generate TractSeg outputs based on the Population Template FOD.
TractSeg will produce track files (.tck), and these can be converted to fixels using tck2fixel (for example, tck2fixel $TractSeg_region_tck $fixel_directory_in $fixel_masks_dir $Region_fixel_mask).
The $Region_fixel_mask can be used as an input to the -mask option when calling the command fixelcfestats (which is essentially saying to conduct the statistical analysis, but only in the region ecompassed by the fixel mask).
Hope this helps! Additional information can be found in this thread
Cheers,
Arkiev