vistalab/dcm-convert repository overview

⁠vistalab/dcm-convert

Converts raw MR DICOM data, from Siemens or GE, to NIfTI.

This container consists of the python package, scitran.data. The run entrypoint is configured to accept a semi-standard input filetype, a tgz, that contains raw data and a json file that indicates the raw data filetype, header data, and metadata corrections and an output base directory where results will be saved.

⁠Usage

vistalab/dcm-convert accepts three inputs: <path_to_dicom_tgz> <outfile_name_prefix> <log_level[=info]>

The following will take the raw, tarred and zipped, DICOM input <input.tgz> and convert it to nifti, <outprefix.nii.gz>.

    docker run --rm -ti \
        -v /path/to/dicom/data:/data \
        vistalab/dcm-convert \
        /data/input.tgz \
        /data/outprefix

⁠Resources

Note that the run command in this container is the ~equivelant to installing Scitran Data⁠ and running the following command in python.

    import scitran.data as scidata
    ds = scidata.parse('/path/to/input.gz', filetype='dicom')
    ds.load_data()
    scidata.write(ds, ds.data, 'outprefix', filetype='nifti')

For more information on using Scitran Data in bash, see the CLI tutorial⁠.

For more information on using Scitran Data in python see the Python tutorial⁠.