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.



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