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philips_to_ismrmrd

Philips to ISMRMRD converter

Build context for a Flywheel Gear which runs the philips_to_ismrmrd tool (v0.1.0). For more information on the ISMRMRD format see ISMRMRD's documentation

  • You can change build.sh to edit the repository name for the image (default=flywheel/philips_to_ismrmrd).
  • The resulting image is ~1GB

Build the Image

To build the image:

git clone https://github.com/flywheel-apps/philips_to_ismrmrd.git
./build.sh

Example Local Usage

To run the philips_to_ismrmrd command in this image on your local instance, do the following:

docker run --rm -ti \
  -v </path/to/raw/data>:/flywheel/v0/input/raw \
  -v </path/to/lab/data>:/flywheel/v0/input/lab \
  -v </path/to/sin/data>:/flywheel/v0/input/sin \
  -v </path/for/output/data>:/flywheel/v0/output \
  flywheel/philips_to_ismrmrd

Usage notes:

  • You are mounting the directories (using the -v flag) which contain the three input data files in directories in the container at /flywheel/v0/input/ and mounting the directory where you want your output data within the container at /flywheel/v0/output.
  • The three input directories are mounted separately within the container. Each input directory should contain only one file (.raw, .sin or .lab)
  • If an alternate stylesheet (.xsl file) for conversion is desired, an optional directory can be mounted with the added line -v </path/to/xsl/data>:/flywheel/v0/input/user_stylesheet
  • No input arguments are required for the container to be executed