Cancer Imaging Phenomics Toolkit (CaPTk)  1.8.1
Image Co-registration

This tool registers multiple moving images to a single target image using the Greedy Registration technique [1]. This tool is also available from the web on the CBICA Image Processing Portal. Please see the experiment on the portal for details. REQUIREMENTS:

1. A Target image.
2. Up to 5 moving images

USAGE:

1. Launch the "Registration" dialog from the "Preprocessing" menu.
2. Customize the parameters (Metrics, Radius and Iterations) as needed; for details regarding the parameters and their usage, please refer to the Greedy manual [2].
3. Specify the moving images (up to 5) and their respective output images.
4. Click on 'Register'.
5. The output image is saved in the specified locations.
6. This can also be used from the command line:
${CaPTk_InstallDir}/bin/Preprocessing.exe -i moving.nii.gz -rFI fixed.nii.gz -o output.nii.gz -reg Affine -rME NCC-2x2x2 -rIS 1 -rNI 100,50,5  More usage options are available via the greedy command-line executable (see documentation for it here), which is present in ${CaPTk_InstallDir}/bin/.

References:

1. P.A.Yushkevich, J.Pluta, H.Wang, L.E.Wisse, S.Das, D.Wolk, "Fast Automatic Segmentation of Hippocampal Subfields and Medical Temporal Lobe Subregions in 3 Tesla and 7 Tesla MRI", Alzheimer's & Dementia: The Journal of Alzheimer's Association, 12(7), P126-127, DOI:10.1016/j.jalz.2016.06.205
2. www.github.com/pyushkevich/greedy