Par0021 - elastix

Registration Description

Registration optimisation for subject-FA images to FA template, multiple data sources

Image data

Rotterdam data:

Oxford data:

Screen shot:



Registration parameters for the registration of subject-FA images to the FMRIB-58 FA template were optimized using an evaluation framework based on the cross-subject similarity of probabilistic tractography tract-maps. The following parameters were optimized: warp field resolution; similarity metric; multiresolution strategy; regularization weight; optimizer; localization of similarity metric. Parameters were varied in an exhaustive fashion, resulting in 576 different parameter settings per datasource.

All experiments and results are described in the accompanying paper. Optimal registration parameters for both datasets are available for download here, as well as a zip archive containing all 576 parameter files, as well as all parameter files used in the optimization of FNIRT.

Registration Settings

For parameter files see the Elastix Model Zoo repository on GitHub.

elastix version: 4.5

Command line call:

elastix -f FMRIB58 -fMask refmask -m FAim -mMask immask -out outdir -p regPoint -t0 affine/TransformParameters.0.txt

Published in

These registrations are described in the publication:

M. de Groot, M.W. Vernooij, M.A. Ikram, F Vos, S.M. Smith, W.J. Niessen and J. Andersson, Improving alignment in Tract-based spatial statistics: Evaluation and optimization of image registration., NeuroImage 76, 400-411


[1] Ikram, M.A., Van der Lugt, A., Niessen, W.J., Krestin, G.P., Koudstaal, P.J., Hofman, A., Breteler, M.M.B., Vernooij, M.W., 2011. The Rotterdam scan study: design and update up to 2012. Eur. J. Epidemiol. 26, 811–824.

[2] Jbabdi, S., Behrens, T.E.J., Smith, S.M., 2010. Crossing fibres in tract-based spatial statistics. NeuroImage 49, 249–256.

© 2020 Viktor van der Valk