All the code used in the development and testing of "Evaluation of surface-based hippocampal registration using ground-truth subfield definitions" written by Jordan DeKraker at McGill University under the supervision of Alan Evans and Boris Bernhardt Each original dataset is in the `BIDS/` directory, including manual segmentations performed by JD. For convenience of viewing, many results are also made available at 100um isotropic resolution. Method summary: HippUnfold (https://github.com/khanlab/hippunfold) (DeKraker et al., 2022) was first used to map all manually segmented hippocampi to a standardized unfolded space and to calculate metrics including thickness, gyrifcation, and curvature. These 2D metric data were then registered. Registrations were applied to manually annotated subfields, and their overlap was calculated. The novel methods used here have now been incorporated into the latest hippunfold release (https://github.com/khanlab/hippunfold/pull/228). As a control condition, volumetric registration was also performed on binarized hippocampal masks. All experiments were conducted in MATLAB, with dependencies included here. Several external dependencies (eg. ANTs, wb_command, etc) are also required, all of which can be found within the HippUnfold singularity image. data organization: BIDS ├── sub-122017 │ └── anat │ ├── sub-122017_blockface-image.nii.gz │ ├── sub-122017_hemi-L_dseg-fullres.nii.gz │ ├── sub-122017_hemi-L_dseg-ManualSubfieldsJD.nii.gz │ ├── sub-122017_hemi-L_dseg.nii.gz │ ├── sub-122017_hemi-L.nii.gz │ ├── sub-122017_hemi-L_space-unfolded_dseg-ManualSubfieldsJD.nii.gz │ ├── sub-122017_hemi-L_space-unfolded.nii.gz │ ├── sub-122017_hemi-L_unfolded.nii.gz │ ├── sub-122017_hemi-R_dseg-fullres.nii.gz │ ├── sub-122017_hemi-R_dseg-ManualSubfieldsJD.nii.gz │ ├── sub-122017_hemi-R_dseg.nii.gz │ ├── sub-122017_hemi-R.nii.gz │ ├── sub-122017_hemi-R_space-unfolded_dseg-ManualSubfieldsJD.nii.gz │ ├── sub-122017_hemi-R_space-unfolded.nii.gz │ └── sub-122017_hemi-R_unfolded.nii.gz ├── sub-152017 │ └── anat │ ├── sub-152017_blockface-image.nii.gz │ ├── sub-152017_hemi-L_dseg-fullres.nii.gz │ ├── sub-152017_hemi-L_dseg-ManualSubfieldsJD.nii.gz │ ├── sub-152017_hemi-L_dseg.nii.gz │ ├── sub-152017_hemi-L.nii.gz │ ├── sub-152017_hemi-L_space-unfolded_dseg-ManualSubfieldsJD.nii.gz │ ├── sub-152017_hemi-L_space-unfolded.nii.gz │ ├── sub-152017_hemi-L_unfolded.nii.gz │ ├── sub-152017_hemi-R_dseg-fullres.nii.gz │ ├── sub-152017_hemi-R_dseg-ManualSubfieldsJD.nii.gz │ ├── sub-152017_hemi-R_dseg.nii.gz │ ├── sub-152017_hemi-R.nii.gz │ ├── sub-152017_hemi-R_space-unfolded_dseg-ManualSubfieldsJD.nii.gz │ ├── sub-152017_hemi-R_space-unfolded.nii.gz │ └── sub-152017_hemi-R_unfolded.nii.gz ├── sub-bbhist │ └── anat │ ├── sub-bbhist_hemi-L_100um.nii.gz │ ├── sub-bbhist_hemi-L_dseg-fullres.nii.gz │ ├── sub-bbhist_hemi-L_dseg-ManualSubfieldsJD_100um.nii.gz │ ├── sub-bbhist_hemi-L_dseg-ManualSubfieldsJD.nii.gz │ ├── sub-bbhist_hemi-L_dseg.nii.gz │ ├── sub-bbhist_hemi-L.nii.gz │ ├── sub-bbhist_hemi-L_space-unfolded_dseg-ManualSubfieldsJD.nii.gz │ ├── sub-bbhist_hemi-L_space-unfolded.nii.gz │ ├── sub-bbhist_hemi-L_unfolded.nii.gz │ ├── sub-bbhist_hemi-R_100um.nii.gz │ ├── sub-bbhist_hemi-R_dseg-fullres.nii.gz │ ├── sub-bbhist_hemi-R_dseg-ManualSubfieldsJD_100um.nii.gz │ ├── sub-bbhist_hemi-R_dseg-ManualSubfieldsJD.nii.gz │ ├── sub-bbhist_hemi-R_dseg.nii.gz │ ├── sub-bbhist_hemi-R-fullres.nii.gz │ ├── sub-bbhist_hemi-R.nii.gz │ ├── sub-bbhist_hemi-R_space-unfolded_dseg-ManualSubfieldsJD.nii.gz │ ├── sub-bbhist_hemi-R_space-unfolded.nii.gz │ └── sub-bbhist_hemi-R_unfolded.nii.gz └── sub-pli3d └── anat ├── sub-pli3d_hemi-L_100um.nii.gz ├── sub-pli3d_hemi-L_dseg-fullres.nii.gz ├── sub-pli3d_hemi-L_dseg-ManualSubfieldsJD_100um.nii.gz ├── sub-pli3d_hemi-L_dseg-ManualSubfieldsJD.nii.gz ├── sub-pli3d_hemi-L_dseg.nii.gz ├── sub-pli3d_hemi-L-fullres.nii.gz ├── sub-pli3d_hemi-L.nii.gz ├── sub-pli3d_hemi-L_space-unfolded_dseg-ManualSubfieldsJD.nii.gz ├── sub-pli3d_hemi-L_space-unfolded.nii.gz └── sub-pli3d_hemi-L_unfolded.nii.gz hippunfold_v1.2.0/hippunfold ├── sub-122017 │ ├── anat │ │ ├── sub-122017_hemi-L_space-corobl_desc-subfields_atlas-bigbrain_dseg.nii.gz │ │ └── sub-122017_hemi-R_space-corobl_desc-subfields_atlas-bigbrain_dseg.nii.gz │ ├── coords │ │ ├── sub-122017_dir-AP_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ ├── sub-122017_dir-AP_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ ├── sub-122017_dir-IO_hemi-L_space-corobl_label-hipp_desc-equivol_coords.nii.gz │ │ ├── sub-122017_dir-IO_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ ├── sub-122017_dir-IO_hemi-R_space-corobl_label-hipp_desc-equivol_coords.nii.gz │ │ ├── sub-122017_dir-IO_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ ├── sub-122017_dir-PD_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ └── sub-122017_dir-PD_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ ├── surf │ │ ├── sub-122017_hemi-L_space-corobl_den-unfoldiso_label-hipp_atlas-bigbrain_subfields.label.gii │ │ ├── sub-122017_hemi-L_space-corobl_den-unfoldiso_label-hipp_curvature.shape.gii │ │ ├── sub-122017_hemi-L_space-corobl_den-unfoldiso_label-hipp_desc-smoothed_midthickness.surf.gii │ │ ├── sub-122017_hemi-L_space-corobl_den-unfoldiso_label-hipp_gyrification.shape.gii │ │ ├── sub-122017_hemi-L_space-corobl_den-unfoldiso_label-hipp_inner.surf.gii │ │ ├── sub-122017_hemi-L_space-corobl_den-unfoldiso_label-hipp_midthickness.surf.gii │ │ ├── sub-122017_hemi-L_space-corobl_den-unfoldiso_label-hipp_outer.surf.gii │ │ ├── sub-122017_hemi-L_space-corobl_den-unfoldiso_label-hipp_subfields-ManualJD.label.gii │ │ ├── sub-122017_hemi-L_space-corobl_den-unfoldiso_label-hipp_surfaces.spec │ │ ├── sub-122017_hemi-L_space-corobl_den-unfoldiso_label-hipp_surfarea.shape.gii │ │ ├── sub-122017_hemi-L_space-corobl_den-unfoldiso_label-hipp_thickness.shape.gii │ │ ├── sub-122017_hemi-L_space-unfolded_den-unfoldiso_label-hipp_inner.surf.gii │ │ ├── sub-122017_hemi-L_space-unfolded_den-unfoldiso_label-hipp_midthickness.surf.gii │ │ ├── sub-122017_hemi-L_space-unfolded_den-unfoldiso_label-hipp_outer.surf.gii │ │ ├── sub-122017_hemi-R_space-corobl_den-unfoldiso_label-hipp_atlas-bigbrain_subfields.label.gii │ │ ├── sub-122017_hemi-R_space-corobl_den-unfoldiso_label-hipp_curvature.shape.gii │ │ ├── sub-122017_hemi-R_space-corobl_den-unfoldiso_label-hipp_desc-smoothed_midthickness.surf.gii │ │ ├── sub-122017_hemi-R_space-corobl_den-unfoldiso_label-hipp_gyrification.shape.gii │ │ ├── sub-122017_hemi-R_space-corobl_den-unfoldiso_label-hipp_inner.surf.gii │ │ ├── sub-122017_hemi-R_space-corobl_den-unfoldiso_label-hipp_midthickness.surf.gii │ │ ├── sub-122017_hemi-R_space-corobl_den-unfoldiso_label-hipp_outer.surf.gii │ │ ├── sub-122017_hemi-R_space-corobl_den-unfoldiso_label-hipp_subfields-ManualJD.label.gii │ │ ├── sub-122017_hemi-R_space-corobl_den-unfoldiso_label-hipp_surfaces.spec │ │ ├── sub-122017_hemi-R_space-corobl_den-unfoldiso_label-hipp_surfarea.shape.gii │ │ ├── sub-122017_hemi-R_space-corobl_den-unfoldiso_label-hipp_thickness.shape.gii │ │ ├── sub-122017_hemi-R_space-unfolded_den-unfoldiso_label-hipp_inner.surf.gii │ │ ├── sub-122017_hemi-R_space-unfolded_den-unfoldiso_label-hipp_midthickness.surf.gii │ │ ├── sub-122017_hemi-R_space-unfolded_den-unfoldiso_label-hipp_outer.surf.gii │ │ ├── sub-122017_space-corobl_den-unfoldiso_label-hipp_atlas-bigbrain_subfields.dlabel.nii │ │ ├── sub-122017_space-corobl_den-unfoldiso_label-hipp_curvature.dscalar.nii │ │ ├── sub-122017_space-corobl_den-unfoldiso_label-hipp_gyrification.dscalar.nii │ │ └── sub-122017_space-corobl_den-unfoldiso_label-hipp_thickness.dscalar.nii │ └── warps │ ├── sub-122017_hemi-L_label-hipp_from-corobl_to-unfold_mode-image_xfm.nii.gz │ ├── sub-122017_hemi-L_label-hipp_from-unfold_to-corobl_mode-image_xfm.nii.gz │ ├── sub-122017_hemi-R_label-hipp_from-corobl_to-unfold_mode-image_xfm.nii.gz │ ├── sub-122017_hemi-R_label-hipp_from-unfold_to-corobl_mode-image_xfm.nii.gz │ └── sub-122017_space-unfold_label-hipp_refvol.nii.gz ├── sub-152017 │ ├── anat │ │ ├── sub-152017_hemi-L_space-corobl_desc-subfields_atlas-bigbrain_dseg.nii.gz │ │ └── sub-152017_hemi-R_space-corobl_desc-subfields_atlas-bigbrain_dseg.nii.gz │ ├── coords │ │ ├── sub-152017_dir-AP_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ ├── sub-152017_dir-AP_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ ├── sub-152017_dir-IO_hemi-L_space-corobl_label-hipp_desc-equivol_coords.nii.gz │ │ ├── sub-152017_dir-IO_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ ├── sub-152017_dir-IO_hemi-R_space-corobl_label-hipp_desc-equivol_coords.nii.gz │ │ ├── sub-152017_dir-IO_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ ├── sub-152017_dir-PD_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ └── sub-152017_dir-PD_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ ├── surf │ │ ├── sub-152017_hemi-L_space-corobl_den-unfoldiso_label-hipp_atlas-bigbrain_subfields.label.gii │ │ ├── sub-152017_hemi-L_space-corobl_den-unfoldiso_label-hipp_curvature.shape.gii │ │ ├── sub-152017_hemi-L_space-corobl_den-unfoldiso_label-hipp_desc-smoothed_midthickness.surf.gii │ │ ├── sub-152017_hemi-L_space-corobl_den-unfoldiso_label-hipp_gyrification.shape.gii │ │ ├── sub-152017_hemi-L_space-corobl_den-unfoldiso_label-hipp_inner.surf.gii │ │ ├── sub-152017_hemi-L_space-corobl_den-unfoldiso_label-hipp_midthickness.surf.gii │ │ ├── sub-152017_hemi-L_space-corobl_den-unfoldiso_label-hipp_outer.surf.gii │ │ ├── sub-152017_hemi-L_space-corobl_den-unfoldiso_label-hipp_subfields-ManualJD.label.gii │ │ ├── sub-152017_hemi-L_space-corobl_den-unfoldiso_label-hipp_surfaces.spec │ │ ├── sub-152017_hemi-L_space-corobl_den-unfoldiso_label-hipp_surfarea.shape.gii │ │ ├── sub-152017_hemi-L_space-corobl_den-unfoldiso_label-hipp_thickness.shape.gii │ │ ├── sub-152017_hemi-L_space-unfolded_den-unfoldiso_label-hipp_inner.surf.gii │ │ ├── sub-152017_hemi-L_space-unfolded_den-unfoldiso_label-hipp_midthickness.surf.gii │ │ ├── sub-152017_hemi-L_space-unfolded_den-unfoldiso_label-hipp_outer.surf.gii │ │ ├── sub-152017_hemi-R_space-corobl_den-unfoldiso_label-hipp_atlas-bigbrain_subfields.label.gii │ │ ├── sub-152017_hemi-R_space-corobl_den-unfoldiso_label-hipp_curvature.shape.gii │ │ ├── sub-152017_hemi-R_space-corobl_den-unfoldiso_label-hipp_desc-smoothed_midthickness.surf.gii │ │ ├── sub-152017_hemi-R_space-corobl_den-unfoldiso_label-hipp_gyrification.shape.gii │ │ ├── sub-152017_hemi-R_space-corobl_den-unfoldiso_label-hipp_inner.surf.gii │ │ ├── sub-152017_hemi-R_space-corobl_den-unfoldiso_label-hipp_midthickness.surf.gii │ │ ├── sub-152017_hemi-R_space-corobl_den-unfoldiso_label-hipp_outer.surf.gii │ │ ├── sub-152017_hemi-R_space-corobl_den-unfoldiso_label-hipp_subfields-ManualJD.label.gii │ │ ├── sub-152017_hemi-R_space-corobl_den-unfoldiso_label-hipp_surfaces.spec │ │ ├── sub-152017_hemi-R_space-corobl_den-unfoldiso_label-hipp_surfarea.shape.gii │ │ ├── sub-152017_hemi-R_space-corobl_den-unfoldiso_label-hipp_thickness.shape.gii │ │ ├── sub-152017_hemi-R_space-unfolded_den-unfoldiso_label-hipp_inner.surf.gii │ │ ├── sub-152017_hemi-R_space-unfolded_den-unfoldiso_label-hipp_midthickness.surf.gii │ │ ├── sub-152017_hemi-R_space-unfolded_den-unfoldiso_label-hipp_outer.surf.gii │ │ ├── sub-152017_space-corobl_den-unfoldiso_label-hipp_atlas-bigbrain_subfields.dlabel.nii │ │ ├── sub-152017_space-corobl_den-unfoldiso_label-hipp_curvature.dscalar.nii │ │ ├── sub-152017_space-corobl_den-unfoldiso_label-hipp_gyrification.dscalar.nii │ │ └── sub-152017_space-corobl_den-unfoldiso_label-hipp_thickness.dscalar.nii │ └── warps │ ├── sub-152017_hemi-L_label-hipp_from-corobl_to-unfold_mode-image_xfm.nii.gz │ ├── sub-152017_hemi-L_label-hipp_from-unfold_to-corobl_mode-image_xfm.nii.gz │ ├── sub-152017_hemi-R_label-hipp_from-corobl_to-unfold_mode-image_xfm.nii.gz │ ├── sub-152017_hemi-R_label-hipp_from-unfold_to-corobl_mode-image_xfm.nii.gz │ └── sub-152017_space-unfold_label-hipp_refvol.nii.gz ├── sub-bbhist │ ├── anat │ │ ├── sub-bbhist_hemi-L_space-corobl_desc-subfields_atlas-bigbrain_dseg.nii.gz │ │ └── sub-bbhist_hemi-R_space-corobl_desc-subfields_atlas-bigbrain_dseg.nii.gz │ ├── coords │ │ ├── sub-bbhist_dir-AP_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ ├── sub-bbhist_dir-AP_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ ├── sub-bbhist_dir-IO_hemi-L_space-corobl_label-hipp_desc-equivol_coords.nii.gz │ │ ├── sub-bbhist_dir-IO_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ ├── sub-bbhist_dir-IO_hemi-R_space-corobl_label-hipp_desc-equivol_coords.nii.gz │ │ ├── sub-bbhist_dir-IO_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ ├── sub-bbhist_dir-PD_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ │ └── sub-bbhist_dir-PD_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz │ ├── surf │ │ ├── sub-bbhist_hemi-L_space-corobl_den-2mm_label-hipp_atlas-bigbrain_subfields.label.gii │ │ ├── sub-bbhist_hemi-L_space-corobl_den-2mm_label-hipp_curvature.shape.gii │ │ ├── sub-bbhist_hemi-L_space-corobl_den-2mm_label-hipp_desc-smoothed_midthickness.surf.gii │ │ ├── sub-bbhist_hemi-L_space-corobl_den-2mm_label-hipp_gyrification.shape.gii │ │ ├── sub-bbhist_hemi-L_space-corobl_den-2mm_label-hipp_inner.surf.gii │&nbs

{"references": ["DeKraker, J., Haast, R. A., Yousif, M. D., Karat, B., Lau, J. C., K\u00f6hler, S., & Khan, A. R. (2022). Automated hippocampal unfolding for morphometry and subfield segmentation with HippUnfold. Elife, 11, e77945."]}