Par0025 - elastix
Registration Description
intra-subject, longitudinal data; rigid + affine + B-spline transformation, advanced normalized correlation metric with a transform bending energy penalty
Image data
- MR 3D multi-contrast mouse brain data
- The registration steps were carried out with the first echo (TE1) image of the MSME sequence
- T2-weighted images were acquired using a Multi Slice Multi Echo sequence (MSME; TR/TE=5,000ms/10ms; 10 echoes), DTI was recorded with an 8-shot spin echo EPI sequence (30 directions; b-value=670s/mm2, and five supplementary A0 images)
- Voxel size 0.14 x 0.14 x 0.4
- Dimension: 128 x 128 x 22
- Acquired with a Bruker Biospin (Ettlingen, Germany) 9.4T scanner
- Stored in MHD format
Screen shot:
An example of a mouse brain dataset co-registered to the template: on the left you see the used template.
Registration Settings
For parameter files see the Elastix Model Zoo repository on GitHub.
elastix
version: 4.500
Description:
- par0025rigid.txt the rigid registration was used to initialize the affine registration in all subjects/time-points
- par0025affine.txt the affine registration was used to initialize the non-rigid registration in all subjects/time-points
All subjects/time-points were registered to the template. So, the template was used as the fixed image. A fixed image mask was always used.
Command line call:
elastix -f FixedImage_i.mhd -m MovingImage_j.mhd -fMask FixedImageMask_i -p par0025.txt -out outputdir
with: = one of {rigid, affine, bspline}
Published in
[1] L. Hammelrath, S. Škokić, A. Khmelinski, A. Hess, N. van der Knaap, M. Staring, B.P.F. Lelieveldt, D. Wiedermann, M. Hoehn, "Morphological maturation of the mouse brain: an in vivo MRI and histology investigation," NeuroImage, 2015
© 2020 Viktor van der Valk