ASL Calibration (asl_calib)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Calibrates ASL perfusion data to absolute CBF units (ml/100g/min) using an M0 calibration image.
Modality: Perfusion image (3D NIfTI) plus M0 calibration image and structural reference.
Typical Use: Converting relative perfusion signals to absolute CBF values.
Key Parameters¶
-i (perfusion image), -c (M0 calibration image), -s (structural image), --mode (voxelwise or reference region), --tr (TR of calibration)
Key Points¶
Two modes: voxelwise (divides each voxel by local M0) or reference region (uses CSF M0 as reference). Reference region mode more robust to coil sensitivity variations.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
calib_image |
File |
Yes | Calibration image (M0/proton density) | -c |
perfusion |
File |
No | CBF image for calibration (ASL native space) | -i |
structural |
File |
No | Structural image (already BETed) | -s |
transform |
File |
No | ASL-to-structural transformation matrix | -t |
mask |
File |
No | Reference mask in calibration image space | -m |
bmask |
File |
No | Brain mask (ASL space) for sensitivity or tissue T1 estimation | --bmask |
output_dir |
string |
No | Output directory name | -o |
output_file |
string |
No | Output filename for calibrated image (requires -i) | --of |
mode |
string |
No | Calibration mode (longtr or satrecov) | --mode |
tissref |
string |
No | Tissue reference type (csf, wm, gm, none) | --tissref |
te |
double |
No | TE used in sequence (ms) | --te |
tr |
double |
No | TR used in calibration sequence (s, default 3.2, longtr mode) | --tr |
cgain |
double |
No | Relative gain between calibration and ASL data (default 1, longtr mode) | --cgain |
t2star |
boolean |
No | Correct with T2* rather than T2 | --t2star |
t1r |
double |
No | T1 of reference tissue (s) | --t1r |
t2r |
double |
No | T2(*) of reference tissue (ms) | --t2r |
t2b |
double |
No | T2(*) of blood (ms) | --t2b |
pc |
double |
No | Partition co-efficient | --pc |
csfmaskingoff |
boolean |
No | Turn off ventricle masking (segmentation only) | --csfmaskingoff |
str2std |
File |
No | Structural to MNI152 linear registration (.mat) | --str2std |
warp |
File |
No | Structural to MNI152 non-linear registration (warp) | --warp |
Accepted Input Extensions¶
- calib_image:
.nii,.nii.gz - perfusion:
.nii,.nii.gz - structural:
.nii,.nii.gz - transform:
.mat - mask:
.nii,.nii.gz - bmask:
.nii,.nii.gz - str2std:
.mat - warp:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
output_directory |
Directory |
$(inputs.output_dir) |
calibrated_perfusion |
File |
$(inputs.output_file).nii.gz, $(inputs.output_file).nii |
log |
File |
asl_calib.log |
err_log |
File |
asl_calib.err.log |
Output Extensions¶
- calibrated_perfusion:
.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¶
- Arterial Spin Labeling > FSL > ASL Processing