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Aligning images with registration-toolkit

This guide provides an introduction to image alignment in registration-toolkit. To follow this tutorial, please download the fixed and moving example images.

Prerequisites

Install registration-toolkit

# get source and dependencies
git clone https://gitlab.com/educelab/registration-toolkit.git
cd registration-toolkit
brew bundle

# build the software
cmake -S . -B build -DCMAKE_BUILD_TYPE=Release
cmake --build build/

# add the build/bin directory to PATH
export PATH=${PATH}:${PWD}/build/bin

Image alignment with automatic landmark selection

# saves the auto-generated landmarks to landmarks.ldm
rt_register -f fixed.jpg -m moving.jpg -o registered.jpg

# generate a diff image with ImageMagick
magick fixed.jpg registered.jpg -compose difference -composite -auto-level registered-diff.jpg

Image alignment with manual landmark selection

Install Landmarks Picker

brew install --no-quarantine educelab/casks/landmarks-picker

Manually select matching landmarks

  1. Open Landmarks Picker
    • On macOS, you may need to right-click the program in the Applications directory and select Open the first time you run the program.
  2. File → Open fixed... and select fixed.jpg.
  3. File → Open moving... and select moving.jpg.
  4. In the image viewers, scroll to zoom in/out and click + drag to pan.
  5. In the bottom of the Landmarks panel, click the + sign to add a new landmark to the list.
  6. Move the images until you find a matching feature in both images. Double-click the matching feature in both images. The coordinates of the landmark should update in the Landmarks panel.
  7. Repeat steps 5 and 6 until you have at least 4 landmarks.
  8. In the bottom of the Landmarks panel, click the save button (looks like a downward arrow) and save your file as landmarks.ldm next to the images.
  9. In the Terminal, run the following command in the same directory as the images (make sure you've run the export command from the installation instsructions):

Run registration with manual landmarks

# register the images
rt_register -f fixed.jpg -m moving.jpg -o registered.jpg -l landmarks.ldm

# generate a diff image with ImageMagick
magick fixed.jpg registered.jpg -compose difference -composite -auto-level registered-diff.jpg

Viewing/editing automatic landmarks

When running rt_register, add --output-ldm {file}.ldm to save the automatically generated landmarks to disk. This file can then be opened in Landmarks Picker using the folder icon in the bottom of the Landmarks panel. When you select a landmark pair in the landmarks list, the image viewers will auto-navigate to make the landmarks visible (make sure to zoom in first.)