Implementation of SINAPPS

[sebastientourbier]

List of SINAPPS to be implemented:

• NLMdenoising
• CorrectSliceIntensity
• SliceBySliceN4BiasFieldCorrection
• SliceBySliceCorrectBiasField
• CorrectSliceIntensity
• IntensityStandardization
• HistogramNormalization
• ImageReconstruction
• TVSuperResolution

Tasks involved for each SINAPP:

• Check if interfaces already implemented by Priscille and Hamza
• Adapt to sinapp framework or implement interface for each program of the Containerized MIALSRTK library listed above.
• Creation of each sinapp underlies the creation of the following files stored under sinapps/<sinapp-name>/ (see sinapps/nlmdenoise/ for an example):
  • The implementation of the run.py script which provides a BIDS app argument parser, the creation of the workflow and the execution of the sinapp.
  • The implementation of the Dockerfile for containerization that describes the computing environment used to execute the workflow based on an Ubuntu 16.04 LTS system. A conda environment.yml is used to facilitate the installation of the python environment.