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