Evaluation of surface-based hippocampal registration using ground-truth subfield definitions
Creators
- 1. Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
- 2. Institute of Neuroscience and Medicine INM-1, Research Centre Jülich, Germany; C. & O. Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich-Heine-University, 40225 Düsseldorf, Germany
- 3. Institute of Neuroscience and Medicine INM-1, Research Centre Jülich, Germany
- 4. Robarts Research Institute, University of Western Ontario, London, Canada
Description
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
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-2mm_label-hipp_midthickness.surf.gii
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-2mm_label-hipp_outer.surf.gii
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-2mm_label-hipp_surfaces.spec
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-2mm_label-hipp_surfarea.shape.gii
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-2mm_label-hipp_thickness.shape.gii
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-unfoldiso_label-hipp_atlas-bigbrain_subfields.label.gii
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-unfoldiso_label-hipp_curvature.shape.gii
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-unfoldiso_label-hipp_desc-smoothed_midthickness.surf.gii
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-unfoldiso_label-hipp_gyrification.shape.gii
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-unfoldiso_label-hipp_inner.surf.gii
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-unfoldiso_label-hipp_midthickness.surf.gii
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-unfoldiso_label-hipp_outer.surf.gii
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-unfoldiso_label-hipp_subfields-ManualJD.label.gii
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-unfoldiso_label-hipp_surfaces.spec
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-unfoldiso_label-hipp_surfarea.shape.gii
│ │ ├── sub-bbhist_hemi-L_space-corobl_den-unfoldiso_label-hipp_thickness.shape.gii
│ │ ├── sub-bbhist_hemi-L_space-unfolded_den-2mm_label-hipp_inner.surf.gii
│ │ ├── sub-bbhist_hemi-L_space-unfolded_den-2mm_label-hipp_midthickness.surf.gii
│ │ ├── sub-bbhist_hemi-L_space-unfolded_den-2mm_label-hipp_outer.surf.gii
│ │ ├── sub-bbhist_hemi-L_space-unfolded_den-unfoldiso_label-hipp_inner.surf.gii
│ │ ├── sub-bbhist_hemi-L_space-unfolded_den-unfoldiso_label-hipp_midthickness.surf.gii
│ │ ├── sub-bbhist_hemi-L_space-unfolded_den-unfoldiso_label-hipp_outer.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-2mm_label-hipp_atlas-bigbrain_subfields.label.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-2mm_label-hipp_curvature.shape.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-2mm_label-hipp_desc-smoothed_midthickness.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-2mm_label-hipp_gyrification.shape.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-2mm_label-hipp_inner.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-2mm_label-hipp_midthickness.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-2mm_label-hipp_outer.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-2mm_label-hipp_surfaces.spec
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-2mm_label-hipp_surfarea.shape.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-2mm_label-hipp_thickness.shape.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-unfoldiso_label-hipp_atlas-bigbrain_subfields.label.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-unfoldiso_label-hipp_curvature.shape.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-unfoldiso_label-hipp_desc-smoothed_midthickness.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-unfoldiso_label-hipp_gyrification.shape.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-unfoldiso_label-hipp_inner.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-unfoldiso_label-hipp_midthickness.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-unfoldiso_label-hipp_outer.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-unfoldiso_label-hipp_subfields-ManualJD.label.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-unfoldiso_label-hipp_surfaces.spec
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-unfoldiso_label-hipp_surfarea.shape.gii
│ │ ├── sub-bbhist_hemi-R_space-corobl_den-unfoldiso_label-hipp_thickness.shape.gii
│ │ ├── sub-bbhist_hemi-R_space-unfolded_den-2mm_label-hipp_inner.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-unfolded_den-2mm_label-hipp_midthickness.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-unfolded_den-2mm_label-hipp_outer.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-unfolded_den-unfoldiso_label-hipp_inner.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-unfolded_den-unfoldiso_label-hipp_midthickness.surf.gii
│ │ ├── sub-bbhist_hemi-R_space-unfolded_den-unfoldiso_label-hipp_outer.surf.gii
│ │ ├── sub-bbhist_space-corobl_den-2mm_label-hipp_atlas-bigbrain_subfields.dlabel.nii
│ │ ├── sub-bbhist_space-corobl_den-2mm_label-hipp_curvature.dscalar.nii
│ │ ├── sub-bbhist_space-corobl_den-2mm_label-hipp_gyrification.dscalar.nii
│ │ ├── sub-bbhist_space-corobl_den-2mm_label-hipp_thickness.dscalar.nii
│ │ ├── sub-bbhist_space-corobl_den-unfoldiso_label-hipp_atlas-bigbrain_subfields.dlabel.nii
│ │ ├── sub-bbhist_space-corobl_den-unfoldiso_label-hipp_curvature.dscalar.nii
│ │ ├── sub-bbhist_space-corobl_den-unfoldiso_label-hipp_gyrification.dscalar.nii
│ │ └── sub-bbhist_space-corobl_den-unfoldiso_label-hipp_thickness.dscalar.nii
│ └── warps
│ ├── sub-bbhist_hemi-L_label-hipp_from-corobl_to-unfold_mode-image_xfm.nii.gz
│ ├── sub-bbhist_hemi-L_label-hipp_from-unfold_to-corobl_mode-image_xfm.nii.gz
│ ├── sub-bbhist_hemi-R_label-hipp_from-corobl_to-unfold_mode-image_xfm.nii.gz
│ ├── sub-bbhist_hemi-R_label-hipp_from-unfold_to-corobl_mode-image_xfm.nii.gz
│ └── sub-bbhist_space-unfold_label-hipp_refvol.nii.gz
└── sub-pli3d
├── anat
│ └── sub-pli3d_hemi-L_space-corobl_desc-subfields_atlas-bigbrain_dseg.nii.gz
├── coords
│ ├── sub-pli3d_dir-AP_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz
│ ├── sub-pli3d_dir-IO_hemi-L_space-corobl_label-hipp_desc-equivol_coords.nii.gz
│ ├── sub-pli3d_dir-IO_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz
│ └── sub-pli3d_dir-PD_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz
├── surf
│ ├── sub-pli3d_hemi-L_space-corobl_den-unfoldiso_label-hipp_atlas-bigbrain_subfields.label.gii
│ ├── sub-pli3d_hemi-L_space-corobl_den-unfoldiso_label-hipp_curvature.shape.gii
│ ├── sub-pli3d_hemi-L_space-corobl_den-unfoldiso_label-hipp_desc-smoothed_midthickness.surf.gii
│ ├── sub-pli3d_hemi-L_space-corobl_den-unfoldiso_label-hipp_gyrification.shape.gii
│ ├── sub-pli3d_hemi-L_space-corobl_den-unfoldiso_label-hipp_inner.surf.gii
│ ├── sub-pli3d_hemi-L_space-corobl_den-unfoldiso_label-hipp_midthickness.surf.gii
│ ├── sub-pli3d_hemi-L_space-corobl_den-unfoldiso_label-hipp_outer.surf.gii
│ ├── sub-pli3d_hemi-L_space-corobl_den-unfoldiso_label-hipp_subfields-ManualJD.label.gii
│ ├── sub-pli3d_hemi-L_space-corobl_den-unfoldiso_label-hipp_surfaces.spec
│ ├── sub-pli3d_hemi-L_space-corobl_den-unfoldiso_label-hipp_surfarea.shape.gii
│ ├── sub-pli3d_hemi-L_space-corobl_den-unfoldiso_label-hipp_thickness.shape.gii
│ ├── sub-pli3d_hemi-L_space-unfolded_den-unfoldiso_label-hipp_inner.surf.gii
│ ├── sub-pli3d_hemi-L_space-unfolded_den-unfoldiso_label-hipp_midthickness.surf.gii
│ ├── sub-pli3d_hemi-L_space-unfolded_den-unfoldiso_label-hipp_outer.surf.gii
│ ├── sub-pli3d_space-corobl_den-unfoldiso_label-hipp_atlas-bigbrain_subfields.dlabel.nii
│ ├── sub-pli3d_space-corobl_den-unfoldiso_label-hipp_curvature.dscalar.nii
│ ├── sub-pli3d_space-corobl_den-unfoldiso_label-hipp_gyrification.dscalar.nii
│ └── sub-pli3d_space-corobl_den-unfoldiso_label-hipp_thickness.dscalar.nii
└── warps
├── sub-pli3d_hemi-L_label-hipp_from-corobl_to-unfold_mode-image_xfm.nii.gz
├── sub-pli3d_hemi-L_label-hipp_from-unfold_to-corobl_mode-image_xfm.nii.gz
└── sub-pli3d_space-unfold_label-hipp_refvol.nii.gz
unfoldedRegistration
├── 1out_1
├── 1out_2
├── 1out_3
├── 1out_4
├── 1out_5
├── 1out_6
├── 1out.png
├── aligned
├── alignedFeats.png
├── aligned_templateView.m
├── align_unfolded.asv
├── align_unfolded.m
├── align_unfolded.m~
├── borderdists.mat
├── borderdists.png
├── deprecated_featureExtract_laminar.m
├── dice.png
├── diceScores.mat
├── evaluate_unfolded_registration_1out.m
├── evaluate_unfolded_registration.m
├── featureExtract_morphological.m
├── HistogramDist.png
├── MaxDist.png
├── maxprobSubfields.png
├── MeanDist.png
├── morphFeatures.png
├── refvol_space-unfolded_desc-2d.nii.gz
├── unaligned
├── unfolded_registration_1out.m
├── unfolded_registration.m
├── unfolded_warps.png
├── warp_mag_subf.mat
└── warp_mag_subf.png
volumetricRegistration
├── aligned
├── Nativespace_registration.m
├── Resample_to_ref.m
├── temaplteView.png
├── template
├── templateCompleteView.png
└── templateView.m
JD-OK_comparison/
├── Comparison.m
├── CoronalSubfields_Dice.png
├── full8_100um_optbal.nii.gz
├── HistogramDist.png
├── inpaintn.m
├── JDKF_100um.nii.gz
├── JDKF-Kedo_sidebyside.png
├── JDKF_unfolded_L.func.gii
├── JDKF_unfolded_R.func.gii
├── Kedo_100um.nii.gz
├── kedo_unfolded_L.func.gii
├── kedo_unfolded_R.func.gii
├── Recon3D.m
├── sample_mask.png
├── slices
├── sourcedata-Kedo
├── UnfoldedSubfields_Dice.png
├── unfoldedSubfields_hemi-L.png
└── unfoldedSubfields_hemi-R.png
NOTEs:
- Some additional folders and files are present in the data release but have been ommitted from this list for simplicity.
- `aligned`, `unaligned`, `template`, `nout_m`, `slices`, and `sourcedata-Kedo` are folders containing additional data but have been shortened here for simplicity.
- Within HippUnfold, `space-corobl` would normally refer to data reoriented to be oblique to the long axis of the hippocampus (needed for automated tissue segmentation). In this case, these files are actually in cropped native space.
For more information on BigBrain source data, see:
https://bigbrainproject.org/maps-and-models.html
https://search.kg.ebrains.eu/instances/Dataset/908c4a94-ff32-4d77-959c-1fdb25a61bef
for more information on AHEAD source data, see:
https://uvaauas.figshare.com/articles/dataset/Ahead_brain_122017_-_3D_reconstructions/16834114
https://uvaauas.figshare.com/articles/dataset/Ahead_brain_152017_-_3D_reconstructions/16834114
Files
README.md
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Additional details
References
- DeKraker, J., Haast, R. A., Yousif, M. D., Karat, B., Lau, J. C., Köhler, S., & Khan, A. R. (2022). Automated hippocampal unfolding for morphometry and subfield segmentation with HippUnfold. Elife, 11, e77945.