siemens_to_ismrmrd

Siemens to ISMRMRD converter

Build context for a Flywheel Gear which runs the siemens_to_ismrmrd tool (v1.0.1). 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/siemens_to_ismrmrd).
• The resulting image is ~1GB

Build the Image

To build the image:

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

Example Local Usage

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

docker run --rm -ti \
  -v </path/to/input/data>:/flywheel/v0/input/dat \
  -v </path/for/output/data>:/flywheel/v0/output \
  flywheel/siemens_to_ismrmrd

Usage notes:

• You are mounting the directory (using the -v flag) which contains the input data 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 input directory should contain only the file you wish to convert (a .dat file)
• If an alternate parameter map (.xml file) for conversion is desired, an optional directory can be mounted with the additional line -v </path/to/xml/data>:/flywheel/v0/input/user_map
• If an alternate stylesheet (.xsl file) for conversion is desired, an optional directory can be mounted with the additional line -v </path/to/xsl/data>:/flywheel/v0/input/user_stylesheet
• No input arguments are required for the container to be executed