# Raw MRI data — too large for git
ds005595-download/
IBRA-SVD/

# nnUNet training workspace — intermediate files and full checkpoints (112 GB)
phase2_nnunet/nnunet_raw/
phase2_nnunet/nnunet_preprocessed/
phase2_nnunet/nnunet_results/

# Inference weights for Docker (hard-linked from nnunet_results; not needed in git)
models/

# Inference / evaluation outputs
phase3_3t_test_results_checkpoint_best/fold_predictions/
phase3_3t_test_results_checkpoint_best/predicted_masks/
phase4_7t_inference_results_checkpoint_best/fold_predictions/
phase4_7t_inference_results_checkpoint_best/predicted_masks/

# Symlinked review package (points to raw data above)
manual_review_package/3T/
manual_review_package/7T/

# NIfTI and model files (catch-all — covered by dirs above but explicit is safer)
*.nii.gz
*.pth
*.npz

# Slurm logs
phase2_nnunet/logs/
phase3_3t_test_results_checkpoint_best/logs/
phase4_7t_inference_results_checkpoint_best/logs/

# Phase A — normalized inputs and intermediate outputs (large NIfTIs)
phase5A_results/phase5A1_WhiteStripe/
phase5A_results/phase5A4_FoldAgreement/
phase5A_results/phase5A5_RecoverSessions/
# threshold_sweep/ results (CSVs) ARE committed — keep them out of the *.nii.gz catch-all above

# Spacing proxy — nnUNet workspaces (keep fold0 checkpoints out of git)
phase6_SpacingProxy_results/fold0_0p7mm/
phase6_SpacingProxy_results/fold0_0p6mm/
# spacing_decision.json IS committed — not excluded here

# Phase B — nnUNet workspace (large)
phase7B_nnunet/nnunet_raw/
phase7B_nnunet/nnunet_preprocessed/
phase7B_nnunet/nnunet_results/
phase7B_nnunet/logs/
phase7B_results/inference_7t/

# Phase C — nnUNet workspace (large)
phase8C_nnunet/nnunet_raw/
phase8C_nnunet/nnunet_preprocessed/
phase8C_nnunet/nnunet_results/
phase8C_nnunet/logs/
phase8C_results/inference_7t/

# Verified 7T labels ARE committed (small, manually curated — precious)
# dataset_info/7t_verified_labels/ intentionally NOT excluded

# Image files
*.png
*.jpg
*.jpeg
*.gif
*.bmp
*.tiff
*.tif
*.svg
*.webp
*.ico

# Python / tooling artifacts
__pycache__/
*.pyc
.ruff_cache/
node_modules/

# Editor / OS
.vscode/
.DS_Store

# Session handoff — never commit
docs/HANDOFF.md
