scitran/dcm2niix repository overview

⁠scitran/dcm2niix

Build context for a Flywheel Gear⁠ to execute dcm2niix.

⁠Description

Chris Rorden's dcm2niix⁠ is a popular tool for converting images from the complicated formats used by scanner manufacturers (DICOM, PAR/REC) to the simple NIfTI format used by many scientific tools. dcm2niix works for all modalities (CT, MRI, PET, SPECT) and sequence types.

⁠Build the Image

To build the image, either download the files from this repo or clone the repo:

docker build --no-cache -t scitran/dcm2niix

⁠Inputs

The input to this gear can be either a zip, a tgz, or a directory containing DICOMs.

⁠Options

Default options are set in manifest.json and copied to the container on build. Defaults are then loaded by the run script when the algorithm is executed.

⁠Example Usage

To run dcm2niix locally from this container you can do the following: Ensure your input file is in it's own directory.

docker run --rm -ti \
    -v </path/to/input/data_dir>:/flywheel/v0/input/dcm2niix_input \
    -v </path/to/output>:/flywheel/v0/output \
    scitran/dcm2niix