Par0026 - elastix
Registration Description
intra-subject, longitudinal data; rigid + affine + B-spline transformation
Image data
- MR 3D multi-contrast rat 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=630s/mm2, and five supplementary A0 images)
- Voxel size 0.145833 x 0.145833 x 0.5
- Dimension: 192 x 192 x 32
- Acquired with a Bruker Biospin (Ettlingen, Germany) 11.7T scanner
- Stored in MHD format
Screen shot:
An example of the co-registered rat brain data: two time-points for subject S1 are shown. On the left we see time-point 14m and on the right time-point 16m.
Application
Registration Settings
For parameter files see the Elastix Model Zoo repository on GitHub.
elastix
version: 4.500
Description:
- par0026rigid.txt the rigid registration was used to initialize the affine registration in all subjects
- par0026affine.txt the affine registration was used to initialize the non-rigid registration in all subjects
A fixed image mask was always used.
Command line call:
elastix -f FixedImage_i.mhd -m MovingImage_j.mhd -fMask FixedImageMask_i -p par0026.txt -out outputdir
with: = one of {rigid, affine, bspline}
Published in
[1] L. Hammelrath, A. Khmelinskii, C. Po, E. Pracht, H. Endepols, H. Backes, C. Schäfer, M. Staring, B.P.F. Lelieveldt and M. Hoehn, "," in preparation, 2016
© 2020 Viktor van der Valk