Evaluation of surface-based hippocampal registration using ground-truth subfield definitions
Bibliographic record
Abstract
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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.013 | 0.036 |
| Meta-epidemiology (narrow) | 0.003 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.004 | 0.003 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.005 | 0.003 |
| Open science | 0.004 | 0.006 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.011 | 0.009 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".