Probabilistic Tractography with Crossing Fibres (probtrackx2)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Probabilistic tractography using fiber orientation distributions from bedpostx to trace white matter pathways.
Modality: BEDPOSTX output directory plus seed mask (3D NIfTI).
Typical Use: White matter connectivity analysis, tract-based statistics.
Key Parameters¶
-x (seed mask), -s (bedpostx merged samples), --dir (output directory), -l (loop check), --waypoints (waypoint masks), --avoid (exclusion mask)
Key Points¶
Requires bedpostx output. Use --omatrix1 for seed-to-voxel connectivity, --omatrix2 for NxN connectivity. Waypoints constrain tractography to specific paths.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
samples_dir |
Directory |
Yes | bedpostX output directory containing merged samples | --samples= |
mask |
File |
Yes | Brain mask in diffusion space | -m |
seed |
File |
Yes | Seed volume or text file of coordinates | -x |
output_dir |
string |
Yes | Output directory | --dir= |
n_samples |
int |
No | Number of samples per voxel (default 5000) | --nsamples= |
n_steps |
int |
No | Number of steps per sample (default 2000) | --nsteps= |
step_length |
double |
No | Step length in mm (default 0.5) | --steplength= |
c_thresh |
double |
No | Curvature threshold (default 0.2) | --cthr= |
fibthresh |
double |
No | Minimum fiber volume fraction (default 0.01) | --fibthresh= |
dist_thresh |
double |
No | Minimum distance threshold in mm | --distthresh= |
loopcheck |
boolean |
No | Enable loop checking | --loopcheck |
onewaycondition |
boolean |
No | Apply waypoint conditions to each direction separately | --onewaycondition |
rand_fib |
int |
No | Fiber sampling strategy (0=max, 1=sample, 2=sample+reject, 3=sample+reject+modulate) | --randfib= |
fibst |
int |
No | Force starting fiber (1-based index) | --fibst= |
waypoints |
File |
No | Waypoint mask (paths must pass through ALL) | --waypoints= |
waycond |
enum |
No | Waypoint condition (AND or OR) | --waycond= |
avoid |
File |
No | Exclusion mask (reject paths through this) | --avoid= |
stop |
File |
No | Stop mask (terminate paths here) | --stop= |
target_masks |
File |
No | List of target masks | --targetmasks= |
os2t |
boolean |
No | Output seeds to targets | --os2t |
xfm |
File |
No | Transformation matrix (seed to diffusion space) | --xfm= |
invxfm |
File |
No | Inverse transformation matrix | --invxfm= |
seedref |
File |
No | Reference image for seed space | --seedref= |
opd |
boolean |
No | Output path distribution | --opd |
pd |
boolean |
No | Output path distribution for each target | --pd |
out |
string |
No | Output file stem | --out= |
omatrix1 |
boolean |
No | Output matrix (seed x seed) | --omatrix1 |
omatrix2 |
boolean |
No | Output matrix (seed x low-res seed) | --omatrix2 |
omatrix3 |
boolean |
No | Output matrix (seed x target) | --omatrix3 |
omatrix4 |
boolean |
No | Output matrix (tract x tract) | --omatrix4 |
network |
boolean |
No | Network mode (seed file is list of seeds) | --network |
simple |
boolean |
No | Track from single voxel coordinates | --simple |
force_dir |
boolean |
No | Use directory as given (don't add .probtrackX) | --forcedir |
verbose |
int |
No | Verbosity level (0, 1, or 2) | -V |
rseed |
int |
No | Random seed | --rseed= |
modeuler |
boolean |
No | Use modified Euler streamlining | --modeuler |
sampvox |
double |
No | Sample sub-voxel tracking starting points | --sampvox= |
Accepted Input Extensions¶
- mask:
.nii,.nii.gz - seed:
.nii,.nii.gz,.txt - waypoints:
.nii,.nii.gz,.txt - avoid:
.nii,.nii.gz - stop:
.nii,.nii.gz - target_masks:
.txt - xfm:
.mat - invxfm:
.mat - seedref:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
output_directory |
Directory |
$(inputs.output_dir) |
fdt_paths |
File |
$(inputs.output_dir)/fdt_paths.nii.gz, $(inputs.output_dir)/fdt_paths.nii |
way_total |
File |
$(inputs.output_dir)/waytotal |
matrix |
File |
$(inputs.output_dir)/fdt_matrix*.dot |
targets |
File[] |
$(inputs.output_dir)/seeds_to_*.nii.gz, $(inputs.output_dir)/seeds_to_*.nii |
log |
File |
probtrackx2.log |
Output Extensions¶
- fdt_paths:
.nii,.nii.gz - way_total:
.txt - matrix:
.dot - targets:
.nii,.nii.gz
Docker Tags¶
Available versions: latest, 6.0.4-patched2, 6.0.4-patched, 6.0.4, 6.0.4-xenial, 5.0.11, 6.0.0, 6.0.1, 5.0.9
Categories¶
- Diffusion MRI > FSL > Tractography