This repository contains the ASL processing pipeline scripts for the Human Connectome Project.

• Prerequisites
• Installation

The HCP list some prerequisites for their pipelines: https://github.com/Washington-University/HCPpipelines/wiki/Installation-and-Usage-Instructions.

The prerequisites specific to this pipeline, along with links to their installation pages, are listed below:

• FSL
• Workbench

To install hcpasl in the current Python environment:

git clone https://github.com/ibme-qubic/hcp-asl.git
cd hcp-asl
python -m pip install --user .

Once installed, the pipeline may be used as a command-line script as follows:

hcp_asl ${SubjectDirectory} ${mt_scaling_factors}

If available, the user can supply a gradient coefficients file for use in gradient distortion correction as follows:

hcp_asl ${SubjectDirectory} ${mt_scaling_factors} -g ${grad_coeffs}
hcp_asl ${SubjectDirectory} ${mt_scaling_factors} --grads ${grad_coeffs}

The distortion correction script can also be called directly:

hcp_asl_distcorr ${StudyDirectory} ${SubjectNumber} (-g ${grad_coeffs})

If the gradient coefficients are not supplied, the script will perform the other motion correction and registration steps without including gradient distortion correction.