prepXact (experimental) ======================= creates XACT surfaces for whole-brain tractography XACT output can be used for fiber tracking using the `track` command with the `xact` option for eXtended Anatomically Constrained Tractography (ACT). XACT builds on the original ACT framework [Smith2012]_ [Yeh2017]_ by including additional options for tractography and surface definitions for applying anatomical constraints to enhance the biological accuracy of tractography. For a detailed description of XACT and its usage, please refer to the `XACT guide <../guide/XACT.html>`__. | **Usage** .. code-block:: bash ./trekker prepXact [OPTIONS] | **Positionals** - ` TEXT:DIR REQUIRED` Path to Freesurfer aseg file - ` FILE REQUIRED` xact output (.vtk). This single file will contains all surfaces combined. | **Options** .. raw:: html

Option	Description
--fslFirst TEXT	Use FSL First results for subcortical and brainstem surfaces
--abnormality TEXT	Path to abnormality mask/surface to include in the XACT output. If an image is used, it will be converted to a surface.
--cereDistThresh FLOAT	Distance threshold from the brain stem to separate cerebellar white matter. Default: 0.5 mm
--enlargeBrainStem FLOAT	Enlarge or shrink brain stem. Default: 5 mm
--inferiorBrainStemCutLevel FLOAT	Cut level for inferior brain stem. Default: 20 mm
--faceArea FLOAT	Average area of output triangles. Default: 0.25 mm^2
--out_l_wm TEXT	Optional left white matter output. (Label = 1)
--out_r_wm TEXT	Optional right white matter output. (Label = 2)
--out_l_gm TEXT	Optional left gray matter output. (Label = 3)
--out_r_gm TEXT	Optional right gray matter output. (Label = 4)
--out_l_sub TEXT	Optional left subcortical output. (Label = 5)
--out_r_sub TEXT	Optional right subcortical output. (Label = 6)
--out_csf TEXT	Optional cerebrospinal fluid output. (Label = 7)
--out_cer_wm TEXT	Optional cerebellar white matter output. (Label = 8)
--out_cer_gm TEXT	Optional cerebellar gray matter output. (Label = 9)
--out_bs TEXT	Optional brain stem output. (Label = 10)
--out_i_bs TEXT	Optional inferior brain stem output. (Label = 11)
--out_abn TEXT	Optional abnormality output. (Label = 12)
--out_bg TEXT	Optional background output. (Label = 13)

| **General options** .. raw:: html

Option	Description
-h, --help	Print this help message and exit.
-n, --numberOfThreads INT	Number of threads.
-v, --verbose TEXT	Verbose level. Options are "quiet", "fatal", "error", "warn", "info", and "debug". Default=info.
-f, --force	Force overwriting of existing file.

**References** .. [Smith2012] `Smith RE, Tournier JD, Calamante F, Connelly A. "Anatomically-constrained tractography: improved diffusion MRI streamlines tractography through effective use of anatomical information." Neuroimage. 2012 Sep 1;62(3):1924-38. `__ .. [Yeh2017] `Yeh, C.H., Smith, R.E., Dhollander, T. and Connelly, A. "Mesh-based anatomically-constrained tractography for effective tracking termination and structural connectome construction."" In Proc ISMRM (Vol. 58). `__