Mapping DICOM to XNAT metadata
XNAT gathers information from DICOM header field to retrieve important metadata. Because these fields are used differently under various conditions, XNAT makes several passes over the headers to gather the required information.From the scanner console, attempts should be made to satisfy the first or second pass rules. From tools like XNAT’s DICOM Browser and DICOM Batch Editor, the third or fourth pass rules may be easier.
In the first pass over the DICOM header content, XNAT looks for all relevant metadata in the Patient Comments field (0010,4000). This is a freeform field that technicians can populate at the console. On Siemens’ Syngo system, the field can be populated from the ‘Additional Information’ box below the patient information (name, date of birth, etc) section. The metadata should be entered as follows:
The metadata fields should be separated by newlines (as above), commas, or semi-colons. All other content is ignored. The metadata values should have no spaces or special characters in them (underscores are ok). Project_ID should match an existing project in the XNAT host to which the images are being sent.
If one or more of the Project, Subject, and Session fields are found, then no further passes are necessary. Otherwise, XNAT continues with its second pass.
Same as above, except using the Study Comments (0032,4000) field. This field is another freeform field entered at the Syngo console under “Study comments”
In the third pass, XNAT looks for each metadata field in individual DICOM fields, as below:
DICOM Tag Tag Name XNAT Field ----------------------------------------------------------------------- (0008,1030) Study Description Project ID (0010,0010) Patient Name Subject ID (0010,0020) Patient ID Session ID
Same as above, except Accession Number (0008,0050) is used Project ID
There is no fifth pass. If after the four passes described above, XNAT has not satisfactorily matched identified the metadata, it leaves these fields marked as invalid in the generated XML document. If no Project was identified, the DICOM files will be placed in the ‘Unidentified’ prearchive box. If project was identified but Subject and/or Session was not, the DICOM files will be placed in the appropriate project prearchive box, but the automatic matching tool will not be functional and additional data entry will be required.
In addition to the default rules, DicomServer allows one additional, user-defined method for identifying the project, using the "project_spec" property. This custom rule is third in precedence, after the Patient Comments and Study Comments rules (1 and 2 above) but before passes 3, 4, and 5. The content of this property should look like this:
(gggg,eeee):regular expression[:optional matching group index]
The first component, (gggg,eeee), is the DICOM attribute to be examined. The second, a regular expression (in the format of java.util.regex.Pattern) is used to match the content of the indicated DICOM attribute. The last, and optional, component, is the matching group index specifying which group in the regular expression should be used as a prospective project name (defaulting to 1, the first matching group).
If the given attribute matches the given pattern, and the prospective project name matches an actual project name in the XNAT instance, then the session is sorted into that matching project.