Arterial spin labeling processing
This module performs all processing of a subject’s perfusion arterial spin labeling MRI (ASL MRI) scan to generate a calibrated map of resting-state cerebral blood flow (CBF). This pipeline is mainly based on a command line tool oxford_asl from the BASIL toolset and uses tools from FSL, AFNI, and ANTs for volume processing.
-proc_asl
Prerequisites 🖐🏼
You need to run -proc_structural
before this stage
Average ASL timeseries to generate a reference image
Calculate binary mask from ASL and M0 calibration scans (separately)
Automatically crop, bias-field correct, skull strip and segment structural image (nativepro)
Run BASIL’s oxford_asl to compute calibrated map of CBF
Reorient ASL reference and CBF images to standard orientation (LPI)
Compute linear registration between ASL and T1-nativepro space
Register processed CBF map to native cortical surface
Terminal:
$ mica-pipe -sub <subject_id> -out <outputDirectory> -bids <BIDS-directory> -proc_asl
Docker command:
$ docker -proc_asl
Optional arguments:
-proc_asl
has several optional arguments:
Optional argument |
Description |
---|---|
|
String to manually identify the main ASL scan for processing (eg. perf/sub-001_<aslScanStr>.nii.gz). Default string is asl. |
|
String to manually identify the main M0 calibration scan for processing (eg. perf/sub-001_<m0ScanStr>.nii.gz). Default string is m0scan. |
Directories created or populated by -proc_asl:
- <outputDirectory>/micapipe/perf
- <outputDirectory>/micapipe/xfms
Files generated by -proc_asl:
- All volumetric processing outputs: - ASL brain mask: <sub>_desc-asl_brain_mask.nii.gz - Skull-stripped mean ASL image (reference image): *<sub>_desc-aslref_brain.nii.gz - Calibrated cerebral blood flow image in absolute units (from oxford_asl): <sub>_desc-preproc_cbf.nii.gz - Calibrated cerebral blood flow image in absolute units in nativepro space: <sub>_space-nativepro_desc-preproc_cbf.nii.gz - ASL registration files are found in <outputDirectory>/micapipe/<sub>/xfms - Affine registration between T1w nativepro and rsfmri space: <sub>_from-asl_to-nativepro_mode-image_desc-affine_0GenericAffine.mat <sub>_from-asl_to-nativepro_mode-image_desc-affine_InverseWarped.nii.gz <sub>_from-asl_to-nativepro_mode-image_desc-affine_Warped.nii.gz