Add additional coregistration step for subcortical regions

[chrisgorgo]

Using this mask: https://dl.dropboxusercontent.com/u/18255196/secondstepmask.nii.gz

Inspired from the approach in LeadDB:

/Users/andreashorn/Downloads/antsdata_Nick/antsRegistration_mod.maci64 --verbose 1 --dimensionality 3 --float 1 \
                 --output [glanat,glanat.nii] --interpolation Linear --use-histogram-matching 1 \
                 --write-composite-transform 1 \
                 --initial-moving-transform [template_t2.nii,anat_t2.nii,1] \
                 --transform Rigid[0.1] \
                 --convergence [1000x500x0x0,1e-6,10] \
                 --shrink-factors 12x8x4x2 \
                 --smoothing-sigmas 4x3x2x1vox \
                 --masks [NULL,NULL] \
                 --metric MI[template_t2.nii,anat_t2.nii,1,32,Regular,0.25] \
                 --transform Affine[0.1] \
                 --convergence [1000x500x0x0,1e-6,10] \
                 --shrink-factors 8x4x2x1 \
                 --smoothing-sigmas 4x3x2x1vox \
                 --masks [NULL,NULL] \
                 --metric MI[template_t2.nii,anat_t2.nii,1,32,Regular,0.25] \
                 --transform SyN[0.3,3.0,0.0] \
                 --convergence [100x50x20x0,1e-6,10] \
                 --shrink-factors 8x4x2x1 \
                 --smoothing-sigmas 4x3x2x1vox \
                 --masks [NULL,NULL] \
                 --metric MI[template_t2.nii,anat_t2.nii,1,32,Regular,0.25] \
                 --transform SyN[0.2,3.0,0.0] \
                 --convergence [20x5,1e-6,10] \
                 --shrink-factors 2x1 \
                 --smoothing-sigmas 1x0vox \
                 --masks [mask_for_second_SyN_step.nii,NULL] \
                 --metric MI[template_t2.nii,anat_t2.nii,1,32,Regular,0.35]

https://github.com/leaddbs/leaddbs/blob/master/ext_libs/ANTs/ea_ants_nonlinear.m

[oesteban]

Seems like a good idea 👍

[oesteban]

Hi @andreashorn, do you happen to keep the mask that Chris showed above? It seems like the dropbox link above and all the links from your discussion in sourceforge with ANTs devs have vanished.

Thanks very much!

[andreashorn]

Hi, sure it's in lead-dbs under /templates/space/MNI_ICBM_2009b_NLIN_ASYM/subcortical/secondstepmask.nii

and I attached it here,

secondstepmask.nii.gz

Citation for the mask is http://www.ajnr.org/content/30/10/1914 if you need one (not necessary to cite the paper I'd think but in case you'd need to point out a reference that is where it originated).

Best, Andy

[oesteban]

Thanks a lot, this is extremely useful. I'll keep you posted about this.

On Sat, Jan 26, 2019, 10:14 Andreas Horn <[email protected] wrote:

Hi, sure it's in lead-dbs under /templates/space/MNI_ICBM_2009b_NLIN_ASYM/subcortical/secondstepmask.nii

and I attached it here,

secondstepmask.nii.gz https://github.com/poldracklab/niworkflows/files/2799328/secondstepmask.nii.gz

Citation for the mask is http://www.ajnr.org/content/30/10/1914 if you need one (not necessary to cite the paper I'd think but in case you'd need to point out a reference that is where it originated).

Best, Andy

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