ASL Quantification¶
ASDRO has a command line function to perform quantification on valid ASL BIDS data, comprising a NIFTI, JSON sidecar and *aslcontext.tsv file
asldro asl-quantify --params /path/to/quant_params.json /path/to/asl.nii.gz /path/to/output_dir
where:
path/to/quant_params
Path to a JSON file (must have extension .json) providing parameters for the quantifiction calculation. If supplied they will override any values that are within the ASL image’s BIDS sidecar. This allows assumed values to be overidden for example. It has the following objects:
- QuantificationModel
(string) defaults to “whitepaper” (see
AslQuantificationFilter
for options)- ArterialSpinLabelingType
(string) “PCASL”, “CASL” or “PASL”
- PostLabelingDelay
(float) The post labeling delay in seconds.
- LabelingDuration
(float) The label duration in seconds (pCASL/CASL only)
- BolusCutOffDelayTime
(float) The bolus cutoff delay time (PASL only)
- LabelingEfficiency
(float) The efficiency of the labeling pulse
- T1ArterialBlood
(float) If not supplied the default value is based on the value of the BIDS field “MagneticFieldStrength”:
- 1.5 Tesla
1.35s
- 3.0 Tesla
1.65s
/path/to/asl.nii.gz
The path to a valid ASL NIFTI file (must have extension .nii or .nii.gz). It is assumed that in the same location there are also corresponding
/path/to/asl.json
and/path/to/aslcontext.tsv
files.path/to/output_dir
The directory to output the generated perfusion rate/CBF maps to, comprising a NIFTI image and JSON sidecar. The files will be given the same filename as the input NIFTI, with ‘_cbf’ appended before the extension.
For more details on implementation see the
asl_quantification()
pipeline.An example of the quant_params.json file is given below:
{ "QuantificationModel": "whitepaper", "PostLabelingDelay": 1.8, "LabelingEfficiency": 0.85, "BloodBrainPartitionCoefficient": 0.9, "T1ArterialBlood": 1.65, "ArterialSpinLabelingType": "PCASL", "LabelingDuration": 1.8, }