Bayesian Inference for Arterial Spin Labeling (BASIL)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Bayesian kinetic model inversion for ASL data using variational Bayes to estimate perfusion and arrival time.
Modality: 4D ASL NIfTI (differenced tag-control or raw tag/control pairs).
Typical Use: Bayesian perfusion quantification with uncertainty estimation.
Key Parameters¶
-i (input ASL), -o (output dir), --tis (inversion times), --casl/--pasl, --bolus (bolus duration), --bat (arterial transit time prior)
Key Points¶
Core kinetic modeling engine used by oxford_asl. Multi-TI data enables arrival time estimation. Spatial regularization improves estimates in low-SNR regions.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input ASL difference data | -i |
output_dir |
string |
Yes | Output directory name | -o |
mask |
File |
Yes | Brain mask | -m |
options_file |
File |
No | FABBER parameter options file | -@ |
model |
string |
No | Model used for analysis (default buxton) | --model |
nlls |
boolean |
No | Do least squares analysis as first step | --nlls |
infertau |
boolean |
No | Infer on bolus length | --infertau |
infert1 |
boolean |
No | Include uncertainty in T1 values | --infert1 |
inferart |
boolean |
No | Infer on arterial compartment | --inferart |
spatial |
boolean |
No | Adaptive spatial smoothing on CBF | --spatial |
fast |
boolean |
No | Single step analysis (use with --spatial) | --fast |
pgm |
File |
No | Gray matter PV map | --pgm |
pwm |
File |
No | White matter PV map | --pwm |
t1im |
File |
No | Voxelwise T1 (tissue) estimates | --t1im |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - mask:
.nii,.nii.gz - options_file:
.txt - pgm:
.nii,.nii.gz - pwm:
.nii,.nii.gz - t1im:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
perfusion |
File |
$(inputs.output_dir)/step*/mean_ftiss.nii.gz, $(inputs.output_dir)/mean_ftiss.nii.gz |
log |
File |
basil.log |
err_log |
File |
basil.err.log |
Output Extensions¶
- perfusion:
.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¶
- Arterial Spin Labeling > FSL > ASL Processing