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March 7, 2019: mincANTS is now simply referred to as ANTS.

 

This page provides parameters for mincANTS ANTS that could give a reasonable transformation between two atlases.

Mutual Information (MI) is generally used for inter-modality registrations and cross correlation (CC) is used for intra modality registrations. If you have two MRI atlases that have different contrast in just one or two structures, it is faster to segment those structures and then run the registration with CC.

Ex-vivo atlas to in-vivo atlas (both MRI)

Here the assumption is that you want to register an ex-vivo atlas to an in-vivo atlas in order to obtain labels for the in-vivo atlas. In this example:

  • invivo-atlas.mnc (minc file for the in-vivo atlas)
  • exvivo-atlas.mnc (minc file for the ex-vivo atlas)
  • 125 micron (resolution of the in-vivo data)

Manual lsq6

Start with a manual lsq6 alignment using register. The first argument to register is the target, the second the source. Your command would look like this:

...

Code Block
> mincresample -like invivo-atlas.mnc -transformation lsq6_trans_from_register.xfm exvivo-atlas.mnc exvivo-atlas_lsq6.mnc

Non-linear

...

ANTS call

Create the gradient magnitude files necessary for mincANTSANTS

Code Block
> mincblur -fwhm 0.125 -gradient exvivo-atlas_lsq6.mnc exvivo-atlas_lsq6_fwhm_0.125
> mincblur -fwhm 0.125 -gradient invivo-atlas.mnc invivo-atlas_fwhm_0.125

Then run the mincANTS ANTS call

Info

If you have a mask, you can add the following flag to the mincANTS ANTS call to include the mask:

-x mask.mnc

Info

And keep in mind that this example deals with 125 micron files. Change the gradient blurring kernel with respect to the resolution of your input files!

Code Block
> mincANTSANTS 3 \
-m CC[exvivo-atlas_lsq6.mnc,invivo-atlas.mnc,1,4] \
-m CC[exvivo-atlas_lsq6_fwhm_0.125_dxyz.mnc,invivo-atlas_fwhm_0.125_dxyz.mnc,1,4] \
-o mincANTSANTS_trans_from_exvivo_to_invivo_SyN_0.4_Gauss_4_1_radius_4.xfm \
-i 100x100x100x100 \
-t SyN[0.4] \
-r Gauss[4,1] \
--number-of-affine-iterations 0

Alternatively you can run the command with slightly different settings for the SyN and Gauss parameters (this allows for less deformation):

Code Block
> mincANTSANTS 3 \
-m CC[exvivo-atlas_lsq6.mnc,invivo-atlas.mnc,1,3] \
-m CC[exvivo-atlas_lsq6_fwhm_0.125_dxyz.mnc,invivo-atlas_fwhm_0.125_dxyz.mnc,1,3] \
-o mincANTSANTS_trans_from_exvivo_to_invivo_SyN_0.1_Gauss_2_1.xfm \
-i 100x100x100x100 \
-t SyN[0.1] \
-r Gauss[2,1] \
--number-of-affine-iterations 0

Or try it with Mutual Information:

Code Block
> mincANTSANTS 3 \
-m MI[exvivo-atlas_lsq6.mnc,invivo-atlas.mnc,1,32] \
-m CC[exvivo-atlas_lsq6_fwhm_0.125_dxyz.mnc,invivo-atlas_fwhm_0.125_dxyz.mnc,1,3] \
-o mincANTSANTS_trans_from_exvivo_to_invivo_MI_SyN_0.1_Gauss_3_1.xfm \
-i 100x100x100x100 \
-t SyN[0.1] \
-r Gauss[3,1] \ 
--number-of-affine-iterations 0