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Analysis.md

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Population variability

  • deviation vector from mean position
  • RMS variation distance in 3D, as well as in rostral-caudal, dorsal-ventral and lateral medial axes.
  • non-isotropy of variation

registration/update_atlas.ipynb

Registration Error

Registration error compared to ChAT labels

  • centroid position error
  • Jaccard index between aligned atlas and ChAT

Computed for after local registration.

registration/evaluate_registration_metrics_v2_compute_deviation_vs_ChAT.ipynb

Registration error compared to expert annotations

  • centroid position error
  • Jaccard index between aligned atlas and expert annotation.
  • voxel value difference

Computed for both after global registration, and after local registration.

registration/evaluate_registration_metrics_v2_compute_deviation_vs_expert.ipynb

Human Correction

Quantify human correction

registration/analyze_human_correction.ipynb

Global to local difference

registration/update_atlas.ipynb

local to human difference

registration/update_atlas.ipynb

Registration Confidence

  • z-score for global and local registration
  • peak width in most uncertain direction:
  • peak width in most certain direction:

registration/measure_confidence_v4.ipynb

/home/yuncong/Dropbox/BrainProjectFiguresByTopic/Registration/confidence/measurements/peakradius_max_normalized_allstacks_allstructures_allsteps_allpools.json