siemens_to_ismrmrd's Introduction

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

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