This page explains how to set up Face Masking as an XNAT pipeline.
Refer to the XNAT pipeline installation manual. We assume here that you’ve installed the mask_face command line tool to /etc/maskface, and your XNAT pipeline catalog is under <pipeline_catalog> directory.
- Have XNAT client tools ArcGet and XNATRestClient available for your XNAT pipelines.
- Copy the contents of /etc/maskface/pipeline to <pipeline_catalog>/maskface.
- Modify <pipeline_catalog>/maskface/maskface_setup.sh to set up mask_face tool environment dependensies.
In the <pipeline_catalog>/maskface/FaceMasking.xml:
- Modify the <location> value in the pipeline descriptor FaceMasking.xml to point to the actual location of the file;
In the <pipeline_catalog>/maskface/resource/mask_face.xml:
- Edit the <pip:location> in <pipeline_catalog>/mask_face/resource/mask_face.xml to point to /etc/maskface/bin;
- Edit the <pip:commandPrefix> to something like “source /etc/maskface/pipeline/maskface_setup.sh; /bin/bash -V.
Setting up the Face Masking pipeline in XNAT
Set up the pipeline according to the XNAT documentation. The pipeline should be run on mrExperimentData datatype. Face masking is effective for high resolution scans only.
Scan IDs: when running the pipeline, the user can select which scans to deface.
Invasiveness: increase or decrease to control the degree of masking and depth of voxel alteration.