MitkSplit4Dto3DImage User Guide

Table of Contents

• Overview
• Usage
  • Required Arguments
  • Optional Arguments
• Details
  • Output Naming Convention
  • Property Handling
• Examples
  • Example 1: Split a 4D image into 3D time frames
  • Example 2: Input with only one time step
• Supported Input and Output Formats
• Errors and Troubleshooting

Overview

MitkSplit4Dto3DImage is a command-line application provided by the Medical Imaging Interaction Toolkit (MITK) for splitting a 4D image into separate 3D images per time point. This tool is useful for dynamic image analysis or when further processing must be applied to individual time frames.

All temporo-spatial properties associated with the input image are preserved and transferred to the respective time-point outputs when possible.

Usage

MitkSplit4Dto3DImage -i <input_file> -o <output_pattern>

Required Arguments

Argument	Short	Type	Description
–input	-i	File	Path to the input 4D image file. If the image has only one time point, it will be saved directly as the output.
–output	-o	File path (pattern)	Output file path pattern. For multiple time steps, a numeric suffix (_0, _1, etc.) is added before the extension.

Optional Arguments

Argument	Short	Type	Description
–help	-h	Flag	Show help text and usage information.

Details

Output Naming Convention

If the input image contains more than one time step, the output filenames will be generated by appending the time step index to the base output filename:

<basename>_0<extension>, <basename>_1<extension>, ...

For example, for output pattern result.nrrd, and an input with 3 time steps:

• result_0.nrrd
• result_1.nrrd
• result_2.nrrd

If the input image contains only one time step, the output will be saved as is, with no suffix added.

Property Handling

Temporo-spatial properties from the input image are preserved and transferred to the corresponding output images when possible:

• Static properties are cloned as-is.
• Time-dependent properties are extracted for the specific time step using MITK’s TemporoSpatialStringProperty interface.

Examples

Example 1: Split a 4D image into 3D time frames

MitkSplit4Dto3DImage -i dynamic_image.nii.gz -o time_frame.nrrd

What happens:

• Each time step in dynamic_image.nii.gz is saved as a separate file:
  • time_frame_0.nrrd
  • time_frame_1.nrrd
  • etc.

Notes:

• Temporo-spatial metadata (e.g., acquisition time or labels) is preserved for each output.

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Example 2: Input with only one time step

MitkSplit4Dto3DImage -i static_image.nrrd -o result.nrrd

What happens:

• Since the image has only one time point, it is saved directly as result.nrrd without modification or suffix.

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Supported Input and Output Formats

All image formats supported by MITK:

• Input: .nrrd, .nii, .nii.gz, .mhd, .mha, .dcm (via DICOM plugin), etc.
• Output: Typically .nrrd, .nii, .nii.gz, .mhd, .mha, depending on the file extension provided.

Errors and Troubleshooting

• If no arguments are provided, the application exits without doing any work.
• An exception is thrown if image loading fails or output cannot be written.
• Ensure all input paths are correct and writable, and that MITK supports the file format.