README.rst

pl-civet

Table of Contents

• pl-civet
  • Abstract
  • Description
  • Agruments
    • Input Files
  • Example
  • Development
• Testing

Abstract

CIVET is an image processing pipeline for fully automated volumetric, corticometric, and morphometric analysis of human brain imaging data (MRI).

http://www.bic.mni.mcgill.ca/ServicesSoftware/CIVET-2-1-0-Introduction

Description

civet_wrapper.py is a ChRIS-based application that runs the CIVET MRI processing pipeline.

Agruments

[-v <level>] [--verbosity <level>]
Verbosity level for app. Not used currently.

[--version]
If specified, print version number.

[--man]
If specified, print (this) man page.

[--meta]
If specified, print plugin meta data.

Input Files

If -id-file is not given, then civet_wrapper.py will attempt to locate all your input files in the specified input directory. ChRIS does not support positional arguments (besides inputDir and outputDir). This is different from running the CIVET_Processing_Pipeline directly, where you are able to give subject IDs (input file prefixes) as positional arguments. When multiple input files are present, they are processed sequentially by CIVET. Input file names must not contain whitespace nor commas.

tl;dr for inputs incoming/*_t1.mnc, don't specify file names via command line.

Example

docker run --rm -v $PWD/in:/incoming -v $PWD/out:/outgoing fnndsc/pl-civet:2.1.1 civet_wrapper -N3-distance 200 -lsq12 -resample-surfaces -thickness tlaplace:tfs:tlink 30:20 -VBM -combine-surface -spawn -run /incoming /outgoing

Development

docker build -t fnndsc/pl-civet .

To learn about cross-platform and multi-architecture builds, see https://github.com/FNNDSC/cookiecutter-chrisapp/wiki/Multi-Architectural-Images#manifest-list

Testing

docker run --rm -w /usr/local/src --entrypoint /usr/bin/python3 fnndsc/pl-civet -m unittest