registration_evaluation_surfaces_2010

Created By Arno Klein arno
registration_evaluation_surfaces_2010 folder Evaluation of volume-based and surface-based brain image registration methods NeuroImage 2010 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 [doi:10.1016/j.neuroimage.2010.01.091] Article: syn3251075 and supplementary material: syn3251080 This directory contains Matlab and Python software to: convert data call registration packages evaluate and analyze results build volume and surface templates 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 label list 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

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