- Generated on Sat Nov 23 2024 02:13:19 for Medical Imaging Interaction Toolkit by
1.8.17
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Medical Imaging Interaction Toolkit
2024.06.99-60d9b802
Medical Imaging Interaction Toolkit
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MITK Segmentation Task Lists are a JSON-based file format defining a list of segmentation tasks. Segmentation tasks consist at least of a path to a reference image (or MITK scene in version 3 or later of the MITK Segmentation Task List file format) and a unique result path. The result path specifies where the final segmentation of the task is expected to be located once it is done.
Optional properties of a segmentation task include a task name and description as well as various presettings for the segmentation like a label name, a list of suggested names and colors for new labels, a label set preset, or even a pre-segmentation to begin with. The complete set of properties is specified further below in the file format specification.
Version 2 of the file format adds support for MITK Forms. Version 3 adds support for MITK scenes. See the file format specification below for more details.
MITK Segmentation Task Lists must be considered experimental at the moment and at least their latest version is prone to change without any prior warning.
MITK Segmentation Task Lists are JSON files containing a JSON object as root, which must contain the two mandatory properties FileFormat and Version:
We also recommend to specify an optional Name that is used in the application if present instead of the plain filename of the JSON file:
The root object must also contain a mandatory Tasks array containing JSON objects that specify the individual tasks of the task list. A minimum task object must consist of Image and Result file paths. Image is a path to the reference image for the task and Result is a path where the final segmentation is expected to be stored once it is done. Paths can be absolute or relative to the MITK Segmentation Task List file.
In addition, tasks can define various optional properties that mainly specify the start conditions for a segmentation:
Name (string): A name for the task.Description (string): A short description/definition of the task.LabelName (string): The name of the first label in a new segmentation that is created for the task on the fly.LabelNameSuggestions (file path): A Label Suggestions JSON file specifying names and optional colors that are suggested to the user for new labels in the segmentation.Preset (file path): A Label Set Preset XML file in MITK's .lsetp file format. The preset is applied to a new segmentation that is created for the task on the fly. We recommend to use the Segmentation plugin to create such label set preset files as described in its user guide.Segmentation (file path): A pre-segmentation that a user can start with or should refine.Dynamic (boolean): In case Image refers to a dynamic (3d+t) image, specifies whether the segmentation should be static (false), i.e. equal for all time steps, or dynamic (true), i.e. individual for each time step.If a task list contains multiple tasks with common properties, they do not have to be specified for each and every task again and again. Instead, the root object may contain an optional Defaults object that is identical in format to the tasks specified above. There is one exception, though: A Defaults object must not contain a Result file path, since result files of tasks must be distinct by definition. As the name indicates, default properties can still be overridden by individual tasks if they are specified explicitly.
The LabelNameSuggestions property of segmentation tasks is supposed to reference a JSON file that consists of an array of objects with a mandatory name property and an optional color property. For example:
The following example is a complete showcase of the properties and features listed above. It defines four tasks, three of which refer to the same reference image so it is specified as default.
Remember that the only task property required to be distinct is Result so you are pretty free in your task design. For simplicity, we chose to define tasks around organs for this example and named the tasks accordingly:
Version 2 of the MITK Segmentation Task List file format adds support for MITK Forms. An MITK Form is a feedback/survey form just like a Google Form for example. A task object (including the Defaults object) can now reference an MITK Forms file to show the form together with a loaded task. A user can then submit their responses per task into a common CSV response file. It is highly recommended to set the Name of a task as it is used in the response file to identify the corresponding task.
In the following example, each task displays a common form for feedback purposes:
The MITK Forms file defines a form asking for any trouble and the possibility to attach screenshots:
The submitted CSV responses might look like the following table:
| "Timestamp" | "Task" | "Did you have any trouble with this case?" | "Optionally take screenshots if you want to illustrate something:" |
|---|---|---|---|
| "2024-09-26T09:15:35Z" | "Case 01" | "Yes" | "screenshots/screenshot_ZDeCZI.png" |
| "2024-09-26T09:23:58Z" | "Case 02" | "No" | "" |
Version 3 of the MITK Segmentation Task List file format adds support for MITK Scenes (*.mitk or *.mitksceneindex files), allowing arbitrary input data in addition to an image.
A task object (including the Defaults object) can now reference an MITK Scene file instead of an image. It is mutually exclusive to the Image field of a task (you cannot have both in a task). This includes implicit mixing of Image and Scene through the optional Defaults JSON object. For example, it is invalid to specify an Image in the Defaults object while specifying a Scene in a Task and vice versa, as the task would end up having both.
Scene is a JSON object consisting of the two mandatory fields Path and Image, as well as an optional field Segmentation:
Path (file path): Mandatory path to the MITK scene file.Image (string): Mandatory name of an image data node in the MITK scene file that is used as reference image for the segmentation.Segmentation (string): Optional name of a segmentation data node in the MITK scene file that is used as pre-segmentation.Make sure to use unique data node names for Image and Segmentation in an MITK scene as otherwise it may result in undefined behavior.
Contrary to Image, if a Scene has a Segmentation (string), it still can be overridden by the Segmentation (file path) of a Task.
In the following example, Scene is specified in the Defaults object so it is used in all tasks. The scene has a pre-segmentation. However, the pre-segmentation of the scene is overridden in the second task by a Segmentation file.
1.8.17