Registration parameters for the Erasmus Glioma Database

Registration Description

interpatient; affine transform; mutual information

Image data

3D MRI data: pre-contrast T1-weighted, post-contrast T1-weighted, T2-weighted and T2-weighted FLAIR
Brain scans of patients with glioma
Transform tumour segmentations based on scan registration
Registration to the ICBM 152 2009a Nonlinear Symmetric atlas
Varying voxel size and dimensions, data obtained from clinical practice

Application

These parameters have been used to register the patients of the Erasmus Glioma Database to the ICBM 152 2009a Nonlinear Symmetric atlas. The Erasmus Glioma Database contains a total of 774 patients with data collected from clinical routine. Pre-contrast T1-weighted and post-contrast T1-weighted scans are registered to the T1-weighted atlas. T2-weighted and T2-weighted FLAIR scans are registered to the T2-weighted atlas.

Screen shots:

T1w-precontrast-scan T1w-postcontrast-scan T2w-scan T2w-FLAIR-scan

From left to right: Pre-contrast T1-weighted scan, post-contrast T1-weighted scan, T2-weighted scan and T2-weighed FLAIR scan. These scans are from patient EGD-0393.

Registration Settings

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

Elastix version: 5.0.0

Description: Parameter file Par0064_rigid.txt contains the parameters for the rigid registration, parameter file Par0064_affine.txt contains the parameters for the affine registration

Command line call:

# Register scan to atlas
# Replace SCAN.nii.gz by the scan file, and ATLAS.nii.gz by the appropriate atlas file (either the T1 or T2 atlas)
elastix -f ATLAS.nii.gz -m SCAN.nii.gz -p Par0064_rigid.txt -p Par0064_rigid.txt
# Transform scan to atlas
transformix -in SCAN.nii.gz -tp TransformParameters.1.txt

# Transforming masks requires setting BSpline order to 0
sed -i 's/(FinalBSplineInterpolationOrder 3)/(FinalBSplineInterpolationOrder 0)/g' TransformParameters.0.txt
sed -i 's/(FinalBSplineInterpolationOrder 3)/(FinalBSplineInterpolationOrder 0)/g' TransformParameters.1.txt

# Replace MASK.nii.gz with the appropriate mask file
transformix -in MASK.nii.gz -tp TransformParameters.1.txt

Published in

Paper to be published, reference will be added at a later time.

References

ICBM 152 Atlas:

VS Fonov, AC Evans, K Botteron, CR Almli, RC McKinstry, DL Collins and BDCG, Unbiased average age-appropriate atlases for pediatric studies, NeuroImage,Volume 54, Issue 1, January 2011, ISSN 1053–8119, DOI: 10.1016/j.neuroimage.2010.07.033

VS Fonov, AC Evans, RC McKinstry, CR Almli and DL Collins, Unbiased nonlinear average age-appropriate brain templates from birth to adulthood, NeuroImage, Volume 47, Supplement 1, July 2009, Page S102 Organization for Human Brain Mapping 2009 Annual Meeting, DOI: 10.1016/S1053-8119(09)70884-5