Terminologies
Overview
The Terminologies module provides a coding system for specifying anatomy, clinical findings, or other clinical terms. For example, the coding system can be used to specify what anatomical parts are stored in a segmentation node. Using standard codes reduces the chance of data-entry errors and improves interoperability. The coding system in Slicer is compatible with coding used in DICOM information objects and allows storing SNOMED-CT (Systematized Nomenclature of Human and Veterinary Medicine - Clinical Terms) or any other terminologies.
The module can store multiple lists of terminology items, such a list is called a context. Terminologies module comes with two contexts for segmentations (Segmentation category and type - DICOM master list / 3D Slicer General Anatomy list) and one for specifying anatomy (Anatomic codes - DICOM master list). The 3D Slicer General Anatomy list is a subset of the DICOM master list, with terms that are associated with the labels in Slicer’s GenericAnatomyColors color table. Custom contexts can also be defined. The contexts were created as part of the QIICR project, in the dcmqi toolkit.
Each item in the segmentation context specifies category (such as “Tissue”, “Physical Object”, “Body Substance”, …), type (such as “Artery”, “Bone”, “Amygdala”, …), an optional modifier (such as “left” and “right”), recommended display color, and for some items anatomical region can be specified as well. Anatomical region is defined by choosing an item from the anatomical context.
Each item in the anatomical context specifies the anatomical region (such as “Anterior Tibial Artery”, “Bladder”, …) and an optional modifier (such as “left” and “right”). Note that in the user interface and programming interface “anatomic” word may be used as a synonym of “anatomical” - in the future these will be all consistently changed to “anatomical” (#5689).
The terminology module can display user interface (called terminology navigator) for choosing a segmentation terminology item. This navigator appears when selecting the “color” of certain types of data nodes (such as models and markups) in the Data module, or when selecting the “color” for a segment in Segment Editor.
Use cases
Define category, type, modifier and anatomical region of a data object, such as model node or markup node, or a segment in a segmentation node, so that it can be identified unambiguously. The associated standardized codes are also saved into DICOM files when the segmentation is saved as a DICOM Segmentation information object.
Panels and their use
The terminology navigator dialog is displayed when double-clicking the color selector box in data trees and lists where the color of the objects is shown in a column as a color swatch. Such selectors are there for data nodes in the Data, Models, Markups modules, and for the segments within segmentation nodes in the Segmentations and Segment Editor modules.
After double-clicking, the basic selector window opens:
It shows the item types in all categories in a searchable list. Custom name and color can be assigned while keeping the selected terminology entry.
Opening up the panes on the left and right, additional options become visible:
Left pane
Allows selection of a subset of categories (all categories selected by default).
On the top, the terminology context can be changed, as well as new ones loaded from
.jsonfiles.
Right pane
Anatomical region can be selected for items that can be located in multiple parts of the body, such as “Blood clot”, “Mass”, or “Cyst”.
How to
Find items: Start typing the name of the category/type/region in the search box above the column.
Load new terminology/anatomical context: click the Load button next to the context drop-down and select JSON from local storage.
Create custom terminology/anatomical context: Start from an existing JSON file, such as the DICOM master list for terminologies or anatomical contexts. Remove the entries you do not need. Validate the JSON file with the validator online tool.