Extracting FD, FC, and FDC using TractSeg

Hi all
I want to use TractSeg to extract FD, FC, and FDC values from diffusion images. Could you please help me with a step-by-step guide?

Thanks in advance

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


Hi Armin,

Just an addition to Arkiev’s comment, remember to reorient your data into FSL’s standard orientation space early in your dMRI analysis (with fslreorient2std or mrconvert -strides -1,2,3) as TractSeg requires your data to be in that orientation. See here: GitHub - MIC-DKFZ/TractSeg: Automatic White Matter Bundle Segmentation


Hi Armin,

To add to the above. A good source of information and scripts can be found here: Meisler_Reading_FBA/fba/bash_scripts at main · smeisler/Meisler_Reading_FBA · GitHub


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Thanks for asking this question, I am also facing this.