MitkStitch3DImages User Guide

Table of Contents

• Overview
• Usage
  • Required Arguments
  • Optional Arguments
• Notes
• Example
• Output
• Error Handling

Overview

This command-line application allows users to map and stitch multiple 3D images into a unified output geometry using optional registrations and interpolation strategies.

Usage

MitkStitch3DImages -i <input1> [<input2> ...] -o <output> [options]

Required Arguments

Argument	Short	Type	Description
--inputs	-i	String List	Paths to one or more input 3D image files to be mapped and stitched.
--output	-o	File	Path to save the fused 3D image output.

Optional Arguments

Argument	Short	Type	Description
--template	-t	File	Path to a reference image. Its geometry will define the geometry of the stitched output image.
--registrations	-r	String List	Paths to registration files (e.g., from registration frameworks). These are used to map each input image to the reference geometry. Must be same count as --inputs. Use an empty string "" for identity registration.
--interpolator	-n	Int	Interpolation type for image mapping (Default: 2). Values: 1: Nearest Neighbour 2: Linear 3: BSpline 3 4: WSinc Hamming 5: WSinc Welch
--strategy	-s	Int	Strategy for stitching (Default: 0). Values: 0: Mean — computes the mean of overlapping pixel values 1: BorderDistance — picks value furthest from input border
--padding	-p	Float	Padding value for areas in the output image not covered by any input (Default: 0.0).
--help	-h	Flag	Display the help text.

Notes

• If the --registrations parameter is not provided, all images are assumed to use identity mappings.
• If --registrations is given, the number of provided registrations must match the number of inputs.
• The application assumes inputs and registrations are ordered correspondingly (i.e., N-th input uses N-th registration).

Example

MitkStitch3DImages \
  -i scan1.nii scan2.nii \
  -r reg1.map "" \
  -t reference.nii \
  -o stitched_output.nii \
  -n 2 \
  -s 0 \
  -p -1024

This will:

• Map scan1.nii using reg1.map
• Use identity transform for scan2.nii
• Stitch both into the geometry defined by reference.nii
• Use linear interpolation and mean stitching
• Assign -1024 to output voxels not covered by any input

Output

A single 3D image file containing the stitched result of all inputs, saved to the path specified with --output.

Error Handling

• If the number of registrations does not match the number of inputs, the application exits with an error.
• Any exceptions during image loading, registration, or saving are logged and will terminate the application with a failure code.