MitkFuse3Dto4DImage User Guide

Table of Contents

• Overview
• Usage
• Required Arguments
• Optional Arguments
• Details
  • Time Geometry Explanation
• Examples
  • Example 1: Basic usage with default time geometry
  • Example 2: Usage with explicit time geometry
  • Example 3: Error due to incorrect time bounds
• Supported Input Formats
• Output Format

Overview

MitkFuse3Dto4DImage is a command-line tool provided by the Medical Imaging Interaction Toolkit (MITK) for fusing a series of 3D images into a 4D image (3D + time). This is particularly useful when creating dynamic datasets from individual time-resolved image acquisitions.

The resulting 4D image can then be further processed as dynamic data in MITK or other compatible platforms.

Usage

MitkFuse3Dto4DImage -i <input1> <input2> ... -o <output> [--time <t0> <t1> <t2> ...]

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Required Arguments

Argument	Short	Type	Description
--inputs	-i	List of files	Paths to input 3D image files to be fused. Must have the same geometry.
--output	-o	File	Output file path for the generated 4D image.

Optional Arguments

Argument	Short	Type	Description
--time	-t	List of numbers	Time bounds in milliseconds. Format: [minBound0 maxBound1 [maxBound2 [...]]]. See examples below. If omitted, a default time geometry is generated with 1 ms per step.
--help	-h	Flag	Show help and usage information.

Details

Time Geometry Explanation

• You must provide N+1 time bounds for N input images.
• The first number defines the start time of the first time step.
• Every subsequent number is a max bound for the preceding time step.

For example, --time 2 3.5 10 used with 2 input images defines:

• Time step 0: from 2 ms to 3.5 ms
• Time step 1: from 3.5 ms to 10 ms

If the number of time bounds does not match the requirement (number_of_inputs + 1), the tool will produce an error.

Examples

Example 1: Basic usage with default time geometry

MitkFuse3Dto4DImage -i image1.nii image2.nii image3.nii -o output4D.nrrd

What happens:

• Fuses image1.nii, image2.nii, and image3.nii into a 4D image.
  
• A default time geometry with start = 0 ms and 1 ms duration per frame is created: [0 1 2 3].

Result:

• 4D output: output4D.nrrd
  
• Time steps:
  
  • Step 0: [0 ms – 1 ms]
    
  • Step 1: [1 ms – 2 ms]
    
  • Step 2: [2 ms – 3 ms]

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Example 2: Usage with explicit time geometry

MitkFuse3Dto4DImage -i image1.nii image2.nii -o output4D.nrrd -t 5 10 20

What happens:

• Fuses two input images.
  
• Time geometry explicitly defined:
  
  • Step 0: [5 ms – 10 ms]
    
  • Step 1: [10 ms – 20 ms]

Result:

• 4D output: output4D.nrrd
  
• Contains two time steps with user-defined timing.

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Example 3: Error due to incorrect time bounds

MitkFuse3Dto4DImage -i image1.nii image2.nii image3.nii -o output4D.nrrd -t 0 1

What happens:

• Input: 3 images → needs 4 time bounds.
  
• Only 2 time bounds provided → the application exits with an error.

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Supported Input Formats

All image formats supported by MITK, e.g.:

• NIfTI (.nii, .nii.gz)
• NRRD (.nrrd)
• DICOM (folder or series)

CAUTION: All input images must have identical geometry (size, spacing, orientation). If the geometries are not equal One can use the apps MITKMapImage and MITKMatchImage to map all images into one referenc geometry (e.g. the first frame).

Output Format

NRRD (.nrrd) or other formats supported by MITK

The output is a single 4D image (3D+t) combining the input volumes.