Oxford ASL Processing Pipeline¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Multi-step pipeline for ASL MRI quantification. Internally chains motion correction, registration, BASIL kinetic modeling, calibration, and partial volume correction.
Modality: 4D ASL NIfTI (tag/control pairs) plus structural T1 image.
Typical Use: Complete ASL quantification from raw data to calibrated CBF maps.
Key Parameters¶
-i (input ASL), -o (output dir), -s (structural image), --casl/--pasl (labeling type), --iaf (input format: tc/ct/diff), --tis (inversion times)
Key Points¶
Handles both pASL and CASL/pCASL. Performs kinetic modeling via BASIL internally. Use --wp for white paper quantification mode. Requires calibration image for absolute CBF.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input ASL data | -i |
output_dir |
string |
Yes | Output directory name | -o |
mask |
File |
No | Mask in native ASL space | -m |
spatial |
boolean |
No | Perform analysis with automatic spatial smoothing of CBF | --spatial |
structural |
File |
No | Structural (T1) image (already BETed) | -s |
casl |
boolean |
No | Data is CASL/pCASL (continuous ASL) rather than pASL | --casl |
artsupp |
boolean |
No | Arterial suppression (vascular crushing) was used | --artsupp |
tis |
string |
No | Inversion times (comma-separated) | --tis |
bolus |
double |
No | Bolus duration (seconds) | --bolus |
bat |
double |
No | Bolus arrival time (seconds) | --bat |
t1 |
double |
No | Tissue T1 value (default 1.3) | --t1 |
t1b |
double |
No | Blood T1 value (default 1.65) | --t1b |
slicedt |
double |
No | Timing difference between slices (default 0) | --slicedt |
calib |
File |
No | Calibration (M0) image | -c |
M0 |
double |
No | Precomputed M0 value | --M0 |
alpha |
double |
No | Inversion efficiency (default 0.98 pASL, 0.85 cASL) | --alpha |
tr |
double |
No | TR of calibration data (default 3.2s) | --tr |
wp |
boolean |
No | Use white paper quantification | --wp |
senscorr |
boolean |
No | Use bias field from segmentation for sensitivity correction | --senscorr |
vars |
boolean |
No | Also save parameter estimated variances | --vars |
report |
boolean |
No | Report mean perfusion within GM mask (requires structural) | --report |
norm |
boolean |
No | Output perfusion maps normalised by GM mean (requires structural) | --norm |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - mask:
.nii,.nii.gz - structural:
.nii,.nii.gz - calib:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
output_directory |
Directory |
$(inputs.output_dir) |
perfusion |
File |
$(inputs.output_dir)/native_space/perfusion.nii.gz |
arrival |
File |
$(inputs.output_dir)/native_space/arrival.nii.gz |
log |
File |
oxford_asl.log |
err_log |
File |
oxford_asl.err.log |
Output Extensions¶
- perfusion:
.nii.gz - arrival:
.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
- Pipelines > FSL > ASL