TIGRLab/mirtk_singularity

Name: mirtk_singularity

Owner: Kimel Family Translational Imaging-Genetics Research Lab

Description: Singularity build for Medical Image Registration ToolKit (MIRTK)

Created: 2017-04-13 16:43:06.0

Updated: 2017-04-13 16:43:06.0

Pushed: 2017-04-13 17:00:12.0

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README

MIRTK Singularity image

A bootstrap definition for a Singularity image based on the Medical Image Registration ToolKit (MIRTK) docker image.

Creating the image requires root:

See Singularity documentation for more information.

1. Create an empty container

sudo singularity create MIRTK.img

1. Bootstrap the container

sudo singularity bootstrap MIRTK.img Singularity.def

Usage

The container is basically a complete environment with the MIRTK toolkit installed.

To obtain shell access to the container

singularity shell MIRTK.img

Two mountpoints are provided: /input /output

These can be used to interact with the local filesystem using the -B option.

To convert a pointset from one format to another:

singularity run -B <src_dir>:/input -B <dst_dir>:/output MIRTK.img convert-pointset /input/<input_file> /output/<output_file>