configure face masking as an XNAT pipeline

This page explains how to set up Face Masking as an XNAT pipeline.

Installation

Prerequisites:


Installation Instructions:

  • 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 dependencies

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. Refer to the XNAT pipeline installation manual

The pipeline should be run on xnat:mrSessionData datatype. Face masking is effective for high resolution scans only.

Pipeline options

OptionDescription
Scan IDsWhen running the pipeline, the user can select which scans to deface
Invasivenessincrease or decrease to control the degree of masking and depth of voxel alteration

$label.name