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Add MNI atlas labeling notebook for AAL3 and Brodmann parcels#169

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emiddell merged 11 commits into
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dev-may
Jun 15, 2026
Merged

Add MNI atlas labeling notebook for AAL3 and Brodmann parcels#169
emiddell merged 11 commits into
devfrom
dev-may

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@mayucel

@mayucel mayucel commented Jun 15, 2026

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  • Demonstrates AAL3 and Brodmann label assignment on both Colin27 and ICBM152 head models.
  • Shows how to visualize atlas labels on pial and inflated brain surfaces.
  • Includes ROI highlighting examples for selected AAL3 and Brodmann regions.
  • Adds MNI coordinate spot-checks for verifying anatomically plausible Brodmann labels.
  • Provides parcel-level summary tables showing how AAL3/Brodmann labels overlap with Schaefer2018 parcels.
  • Includes an optional SAVE_TABLES example for exporting the four parcel summary tables as TSV files.

mayucel and others added 10 commits May 9, 2026 19:43
Update 52_custom_parcel_labels.ipynb so the final ICBM152 summary table reports Brodmann labels instead of repeating the AAL3 summary.
Deleted the original notebooks:
- examples/head_models/52a_aal3_labels_colin27_and_icbm152.ipynb
- examples/head_models/52b_brodmann_labels_icbm152_and_colin27.ipynb

Updated Eike's combined notebook by:
- Renaming it from 52_custom_parcel_labels.ipynb to 52_mni_atlas_labels_aal3_brodmann.ipynb so AAL3 and Brodmann are easier to find for users
- Updating the notebook heading to clearly mention AAL3 and Brodmann atlas labels
- Adding a short opening sentence explaining that the notebook labels Colin27 and ICBM152 surfaces and summarizes overlap with Schaefer2018 parcels
- Added an optional SAVE_TABLES example that writes the four parcel summary tables to TSV files
@mayucel mayucel requested a review from emiddell June 15, 2026 14:18
@emiddell emiddell merged commit a543442 into dev Jun 15, 2026
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@emiddell emiddell deleted the dev-may branch June 15, 2026 14:45
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3 participants