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
`-aslScanStr` `<str>`	String to manually identify the main ASL scan for processing (eg. perf/sub-001_<aslScanStr>.nii.gz). Default string is asl.
`-m0ScanStr` `<str>`	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