This guide describes how to use the MitkFileConverter to export and import multilabel segmentations using the MITK segmentation stack format.

Prerequisites

Ensure you have:

A working build of MITK including the MitkFileConverter tool.
Input segmentation files in .nrrd or DICOM (.dcm) format.

Use Case 1: Export a Multilabel Segmentation to a Stack of Label Images (NIfTI)

Goal

Convert a MultiLabelSegmentation (e.g., input.nrrd) into:

A stack of NIfTI images (one per label).
A .mitklabel.json file describing the stack.

Output Example

MySegmentation_Label_1.nii.gz
MySegmentation_Label_2.nii.gz
MySegmentation.mitklabel.json

Command

For Bash / Linux / macOS / WSL (Unix-like shells) / PowerShell:

MITKFileConverter \
  -i input_segmentation.nrrd \
  -o ./MySegmentation.nii.gz \
  --output-options '{"Save strategy": "instance", "Instance value": "original"}'

For Windows Command Prompt (cmd.exe):

MITKFileConverter \
  -i input_segmentation.nrrd \
  -o ./MySegmentation.nii.gz \
  --output-options "{""Save strategy"": ""instance"", ""Instance value"": ""original""}"

Options

Option	Value	Description
`Save strategy`	`instance`	Save one image per label
`Instance value`	`original`	Use the label’s value in the image (not binary masks)

You can also use:

Instance value = binary to export binary masks (value = 1)

Use Case 2: Import a Stack and Convert to a Multilabel Segmentation (.nrrd)

Goal

Convert a segmentation stack described by a .mitklabel.json file into a single .nrrd file storing the entire MultiLabelSegmentation.

Input Example

MySegmentation_Label_1.nii.gz
MySegmentation_Label_2.nii.gz
MySegmentation.mitklabel.json

Command

MITKFileConverter \
  -i ./MySegmentation.mitklabel.json \
  -o ./output_segmentation.nrrd

Notes

The converter will auto-detect and combine label images based on the .json metadata.
The output will be a standard MITK-compatible multilabel .nrrd.

Tips & Tricks

You can use .nii.gz, .nrrd, or other ITK-supported formats.
To export using group images instead of per-label masks:

--output-options "Save strategy"="group"

Reference

See the MITK MultiLabel Segmentation Stack Format README for more information about JSON structure, label properties, and file mappings.