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.
Usage
./trekker prepXact [OPTIONS] <FreesurferFolder> <Output_xact_file>
Positionals
<Freesurfer_folder> TEXT:DIR REQUIRED Path to Freesurfer aseg file
<Output_xact_file> FILE REQUIRED xact output (.vtk). This single file will contains all surfaces combined.
Options
| 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
| 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
