Par0033 - elastix

Registration Description

inter-subject; rigid + affine + B-spline transformation; mutual information metric with a transform bending energy penalty

Image data

Ex vivo MRI on mouse skulls to image the brain
T1 3D Flash sequence
TR 15ms, TE 5.3ms, NA 12, matrix 256186186, FOV 181813cm, hermite FA 30º, resolution 70µm/pixel, total scan time 58min48s
Voxel size 0.0703125 x 0.07 x 0.07
Acquired with a Bruker Biospin (Ettlingen, Germany) 7T scanner
With a circular polarized MRI transceiver coil for 1H with an inner diameter of 23 mm and Paravision 5.1 software
Stored in MHD format

Screen shot:

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An example of the co-registered mouse brain data: on the left you see the used template.

Application

Registration Settings

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

elastix version: 4.500

Description:

par0033rigid.txt the rigid registration was used to initialize the affine registration in all subjects
par0033similarity.txt the affine registration was used to initialize the non-rigid registration in all subjects

All the data was registerd to a template image. The template image was 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 par0033.txt -out outputdir

with: = one of {rigid, similarity, bspline}

Published in

[1] [D.I. Bink, K. Ritz, C. Mackaaij, A. Khmelinskii, O.J. de Boer, L.M. Gierman, J.C. Sluimer, L. van der Weerd, M.J.A.P. Daemen, "Neuropathology in mouse models for atherosclerosis," Submitted 2016]

[2] [B. Kogelman et al., "," in preparation 2016]