Dorsal Raphe (Supratrochlear subnucleus) mask in MNI-space (ICBM 2009b)
Bibliographic record
Abstract
Here we present a binary mask for Dorsal Raphe, specifically the more dorsal supratrochlear nucleus. The mask was created by combining histological descriptions of DR (Baker, Halliday and Törk, 1990; Baker et al., 1991) and the Allen Human Brain Atlas (Ding et al., 2016), with the MNI-warped BigBrain (Amunts et al., 2013; Xiao et al., 2019). A spherical ROI (3mm radius) was drawn around MNI coordinates x: 0, y: -30, z: -13. Any edge voxels close to the cerebral aqueduct of periaqueductal grey were trimmed leaving a roughly spherical ROI of volume ~32mm3. This position was chosen to align with the supratrochlear subnucleus of DR where neurofibrillary tangles have been identified in asymptomatic stages of Alzheimer’s disease.(Grinberg et al., 2009). The mask is provided in MNI space (ICBM 2009b Nonlinear Asymmetric 0.5mm) which can be downloaded here: https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 . Amunts, K. et al. (2013) ‘BigBrain: an ultrahigh-resolution 3D human brain model’, Science (New York, N.Y.), 340(6139), pp. 1472–1475. Available at: https://doi.org/10.1126/science.1235381.Baker, K.G. et al. (1991) ‘Cytoarchitecture of serotonin-synthesizing neurons in the pontine tegmentum of the human brain’, Synapse (New York, N.Y.), 7(4), pp. 301–320. Available at: https://doi.org/10.1002/syn.890070407.Baker, K.G., Halliday, G.M. and Törk, I. (1990) ‘Cytoarchitecture of the human dorsal raphe nucleus: HUMAN DORSAL RAPHE’, Journal of Comparative Neurology, 301(2), pp. 147–161. Available at: https://doi.org/10.1002/cne.903010202.Ding, S.-L. et al. (2016) ‘Comprehensive cellular-resolution atlas of the adult human brain’, Journal of Comparative Neurology, 524(16), pp. 3127–3481. Available at: https://doi.org/10.1002/cne.24080.Grinberg, L.T. et al. (2009) ‘The dorsal raphe nucleus shows phospho-tau neurofibrillary changes before the transentorhinal region in Alzheimer’s disease. A precocious onset?’, Neuropathology and Applied Neurobiology, 35(4), pp. 406–416. Available at: https://doi.org/10.1111/j.1365-2990.2008.00997.x.Xiao, Y. et al. (2019) ‘An accurate registration of the BigBrain dataset with the MNI PD25 and ICBM152 atlases’, Scientific Data, 6(1), p. 210. Available at: https://doi.org/10.1038/s41597-019-0217-0.
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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 | 0.001 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.045 | 0.016 |
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".