Evaluation of volume-based and surface-based brain image registration methods.
[PDF] [doi:10.1016/j.neuroimage.2010.01.091]
Supplementary Material
Code (convert data, call registration packages, evaluate and analyze results):
Template building scripts:
Data:
Updates:
Registration evaluation studies conducted since this article was published:
Arno Klein, Satrajit S. Ghosh, Brian Avants, B.T.T. Yeo, Bruce Fischl,
Babak Ardekani, James C. Gee, J.J. Mann, Ramin V. Parsey.
2010. NeuroImage. 51: 214-220.
PMCID: PMC2862732
[PDF] [doi:10.1016/j.neuroimage.2010.01.091]
Supplementary Material
Code (convert data, call registration packages, evaluate and analyze results):
Code (Matlab and Python) run on the LPBA40 individuals: LPBA40.tar.gz
Code (Matlab and Python) run on the FS40 individuals: FS40.tar.gz
Code (Matlab and Python) run on the FS40 individuals: FS40.tar.gz
Template building scripts:
FreeSurfer (Python): make_freesurfer_template.txt
ANTS/SyN (the buildtemplateparallel.sh script supercedes this implementation): make_syn_templates.tar.gz
Spherical Demons software (complete version used in this study): SDv1.1-svn593-klein.tar.gz
ANTS/SyN (the buildtemplateparallel.sh script supercedes this implementation): make_syn_templates.tar.gz
Spherical Demons software (complete version used in this study): SDv1.1-svn593-klein.tar.gz
Data:
LPBA label list and
(unlabeled) LPBA40 custom templates (each with 20 brains) (95 MB)
Updates:
2/2010: We have since found much better affine initialization for SyN registrations
by including the following --number-of-affine-iterations argument at the end of the "ANTS" command:
Warp: ANTS 3 -m CC[target.nii.gz, source.nii.gz, 1, 2] -o output_transform.nii.gz
-r Gauss[2,0] -t SyN[0.5] -i 30x99x11 --use-Histogram-Matching
--number-of-affine-iterations 10000x10000x10000x10000x10000
Reslice: WarpImageMultiTransform 3 labeled_source.nii.gz output_labels.nii.gz
-R target.nii output_transformWarp.nii.gz output_transformAffine.txt -use-NN
7/2010: standalone python algorithm for "paired indifference-zone" ranking: rank_paired_indifferencezone.py
(We used this new program to corroborate some of the permutation test results in the study.)
3/2011: LPBA40 ANTs template (all 40 brains) (5.5 MB)
Also see Satrajit Ghosh's ANTs pediatric template.
by including the following --number-of-affine-iterations argument at the end of the "ANTS" command:
Warp: ANTS 3 -m CC[target.nii.gz, source.nii.gz, 1, 2] -o output_transform.nii.gz
-r Gauss[2,0] -t SyN[0.5] -i 30x99x11 --use-Histogram-Matching
--number-of-affine-iterations 10000x10000x10000x10000x10000
Reslice: WarpImageMultiTransform 3 labeled_source.nii.gz output_labels.nii.gz
-R target.nii output_transformWarp.nii.gz output_transformAffine.txt -use-NN
7/2010: standalone python algorithm for "paired indifference-zone" ranking: rank_paired_indifferencezone.py
(We used this new program to corroborate some of the permutation test results in the study.)
3/2011: LPBA40 ANTs template (all 40 brains) (5.5 MB)
Also see Satrajit Ghosh's ANTs pediatric template.
Registration evaluation studies conducted since this article was published:
EMPIRE: Evaluation of Methods for Pulmonary Image Registration 2010 (MICCAI 2010 challenge workshop)