This app performs a recursive walk down an input tree, and for each DICOM file (as filtered with a -e .dcm), will perform an edit or substitution on a pattern of user specified DICOM tags. Resultant edited files are saved in the corresponding location in the output tree. This page is not the canonical reference for pfdicom_tagSub on which this plugin is based. Please see https://github.com/FNNDSC/pfdicom_tagSub for detail about the actual tag substitution process and the pattern of command line flags.

Note that the only different between this plugin and the reference pfdicom_tagSub is that the reference has explicit flags for inputDir and outputDir while this plugin uses positional arguments for the same.

docker run -it --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing  \
        fnndsc/pl-pfdicom_tagsub dcm_tagSub.py                      \
        --tagStruct '
        {
            "PatientName":       "anonymized",
            "PatientID":         "%_md5|7_PatientID",
            "AccessionNumber":   "%_md5|10_AccessionNumber",
            "PatientBirthDate":  "%_strmsk|******01_PatientBirthDate"
        }
        ' --threads 0 -v 2 -e .dcm                                  \
        /incoming /outgoing

Assuming that $(pwd)/in contains a tree of DICOM files, then the above will generate, for each leaf directory node in $(pwd)/in that contains files satisfying the search constraint of ending in .dcm, new DICOM files with the above tag subsitutions: The PatientName is set to anonymized, the PatientID is replaced with the first seven chars of an md5 hash of the original PatientID -- similarly for the AssessionNumber. Finally the PatientBirthDate is masked so that the birthday is set to the first of the month.

Invariably, some debugging will be required. In order to debug efficiently, map the following into their respective locations in the container:

docker run -it --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
        -v $(pwd)/dcm_tagSub/dcm_tagSub.py:/usr/src/dcm_tagSub/dcm_tagSub.py  \
        -v $(pwd)/dcm_tagSub/pfdicom_tagSub.py:/usr/local/lib/python3.5/dist-packages/pfdicom_tagSub/pfdicom_tagSub.py \
        fnndsc/pl-pfdicom_tagsub dcm_tagSub.py                          \
        --tagStruct '
        {
            "PatientName":       "anonymized",
            "PatientID":         "%_md5|7_PatientID",
            "AccessionNumber":   "%_md5|10_AccessionNumber",
            "PatientBirthDate":  "%_strmsk|******01_PatientBirthDate"
        }
        ' --threads 0 -v 2 -e .dcm                                      \
        /incoming /outgoing

This assumes that the source code the underlying pfdicom_tagSub.py module is accessible as shown.

Make sure that the host $(pwd)/out directory is world writable!