fastmonai-upstream-guide

name	fastmonai-upstream-guide
description	Consult MONAI, TorchIO, and nnU-Net documentation and source code for implementation guidance in fastMONAI. Use this skill proactively when implementing new transforms, loss functions, metrics, preprocessing pipelines, or patch-based workflows. Helps ensure fastMONAI implementations align with upstream library patterns and medical imaging best practices.

fastMONAI Upstream Implementation Guide

This skill provides implementation guidance by consulting MONAI, TorchIO, and nnU-Net patterns via live documentation and source code fetching.

When to Use This Skill

Use this skill proactively when:

• Implementing new transforms or augmentations
• Adding loss functions or metrics
• Working on patch-based training/inference workflows
• Establishing preprocessing or postprocessing pipelines
• Ensuring consistency with upstream library conventions

Library-to-Module Mapping

fastMONAI Module	Primary Upstream	What to Check
vision_augmentation	TorchIO	Transform classes, wrapper patterns
vision_metrics	MONAI + nnU-Net	Metric functions, accumulated patterns
vision_loss	MONAI	Loss class signatures, parameters
vision_patch	TorchIO	Queue, Sampler, GridAggregator
vision_core	TorchIO	ScalarImage, LabelMap, resampling

Documentation URLs

TorchIO

• Main docs: https://torchio.readthedocs.io/
• Transforms: https://torchio.readthedocs.io/transforms/transforms.html
• Augmentation: https://torchio.readthedocs.io/transforms/augmentation.html
• Preprocessing: https://torchio.readthedocs.io/transforms/preprocessing.html
• Patch-based: https://torchio.readthedocs.io/patches/index.html

MONAI

• Main docs: https://docs.monai.io/
• Metrics: https://docs.monai.io/en/stable/metrics.html
• Losses: https://docs.monai.io/en/stable/losses.html
• Transforms: https://docs.monai.io/en/stable/transforms.html

nnU-Net v2

• Repository: https://github.com/MIC-DKFZ/nnUNet (complete rewrite of v1, Apache 2.0)
• Documentation index: https://github.com/MIC-DKFZ/nnUNet/tree/master/documentation
• How to use: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/how_to_use_nnunet.md
• Dataset format: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/dataset_format.md
• Extending nnU-Net: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/extending_nnunet.md
• Normalization explained: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/explanation_normalization.md
• Plans files explained: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/explanation_plans_files.md
• Pretraining/finetuning: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/pretraining_and_finetuning.md
• Region-based training: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/region_based_training.md
• Ignore label: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/ignore_label.md
• ResEnc presets: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/resenc_presets.md

Source Code URLs (for implementation details)

TorchIO GitHub

• Transforms base: https://raw.githubusercontent.com/fepegar/torchio/main/src/torchio/transforms/transform.py
• Spatial transforms: https://raw.githubusercontent.com/fepegar/torchio/main/src/torchio/transforms/augmentation/spatial/
• Intensity transforms: https://raw.githubusercontent.com/fepegar/torchio/main/src/torchio/transforms/augmentation/intensity/
• Queue: https://raw.githubusercontent.com/fepegar/torchio/main/src/torchio/data/queue.py
• GridSampler: https://raw.githubusercontent.com/fepegar/torchio/main/src/torchio/data/sampler/grid.py

MONAI GitHub

• Metrics: https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/monai/metrics/meandice.py
• Hausdorff: https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/monai/metrics/hausdorff_distance.py
• Losses: https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/monai/losses/

nnU-Net v2 GitHub (source code)

• Package root: https://github.com/MIC-DKFZ/nnUNet/tree/master/nnunetv2
• Preprocessing root: https://github.com/MIC-DKFZ/nnUNet/tree/master/nnunetv2/preprocessing
• Normalization schemes: https://raw.githubusercontent.com/MIC-DKFZ/nnUNet/master/nnunetv2/preprocessing/normalization/default_normalization_schemes.py
• Resampling: https://github.com/MIC-DKFZ/nnUNet/tree/master/nnunetv2/preprocessing/resampling
• Training root: https://github.com/MIC-DKFZ/nnUNet/tree/master/nnunetv2/training
• Base trainer: https://raw.githubusercontent.com/MIC-DKFZ/nnUNet/master/nnunetv2/training/nnUNetTrainer/nnUNetTrainer.py
• Trainer variants: https://github.com/MIC-DKFZ/nnUNet/tree/master/nnunetv2/training/nnUNetTrainer/variants
• Dice loss: https://raw.githubusercontent.com/MIC-DKFZ/nnUNet/master/nnunetv2/training/loss/dice.py
• Compound losses (DC+CE, DC+BCE, DC+TopK): https://raw.githubusercontent.com/MIC-DKFZ/nnUNet/master/nnunetv2/training/loss/compound_losses.py
• Robust CE loss: https://raw.githubusercontent.com/MIC-DKFZ/nnUNet/master/nnunetv2/training/loss/robust_ce_loss.py
• Deep supervision loss: https://raw.githubusercontent.com/MIC-DKFZ/nnUNet/master/nnunetv2/training/loss/deep_supervision.py
• Evaluation metrics: https://raw.githubusercontent.com/MIC-DKFZ/nnUNet/master/nnunetv2/evaluation/evaluate_predictions.py

Workflow Steps

1. Identify the implementation area

   • Transform/augmentation → TorchIO
   • Metric → MONAI (compute functions) + nnU-Net (accumulated patterns)
   • Loss function → MONAI
   • Patch workflow → TorchIO (Queue, GridSampler)
   • Preprocessing/normalization → nnU-Net v2 conventions
   • Sliding window inference → nnU-Net v2 (Gaussian weighting, tile step size)
   • Evaluation metrics → nnU-Net v2 (TP/FP/FN accumulation, Dice, IoU)

2. Fetch relevant documentation Use WebFetch to retrieve the appropriate documentation page from the URLs above.

3. Fetch source code if needed For implementation details, fetch the raw GitHub file to see:

   • Function signatures and parameters
   • Default values and conventions
   • Internal implementation logic

4. Identify the pattern

   • What parameters does the upstream function accept?
   • What tensor shapes does it expect?
   • What are the default behaviors?

5. Apply to fastMONAI context

   • Make changes in nbs/*.ipynb notebooks (not .py files)
   • Follow existing wrapper patterns
   • Run nbdev_prepare after changes

fastMONAI-Specific Conventions

Transform Wrappers

All transform wrappers must expose .tio_transform property:

class MyTransform(DictTransform):
    def __init__(self, ...):
        self._transform = tio.SomeTransform(...)

    @property
    def tio_transform(self):
        return self._transform

Padding Mode

Always use padding_mode=0 (zero padding) for CropOrPad - this aligns with nnU-Net standards:

tio.CropOrPad(target_size, padding_mode=0)  # Correct
tio.CropOrPad(target_size)  # Avoid - uses TorchIO default

Tensor Shape Conventions

• MONAI metrics expect: [B, C, D, H, W]
• TorchIO uses: [C, D, H, W] for single images
• fastMONAI MedImage/MedMask: 4D tensors with affine tracking

Accumulated Metrics (nnU-Net v2 pattern)

For patch-based training, use accumulated TP/FP/FN rather than per-batch averaging:

class AccumulatedDice(Metric):
    # Accumulates across batches, not averages

nnU-Net v2 Quick Reference

Architecture: The nnunetv2/ package is organized into: preprocessing, training, inference, evaluation, experiment_planning, postprocessing, utilities.

Normalization schemes (in default_normalization_schemes.py):

• ZScoreNormalization - z-score with optional foreground masking (default for MR)
• CTNormalization - clip to 0.5th-99.5th percentiles then z-score (for CT)
• NoNormalization - passthrough (dtype conversion only)
• RescaleTo01Normalization - min-max to [0,1]
• RGBTo01Normalization - divide uint8 by 255

Loss functions (in training/loss/):

• SoftDiceLoss(apply_nonlin, batch_dice, do_bg, smooth=1.0, ddp, clip_tp) - standard soft Dice
• MemoryEfficientSoftDiceLoss - same API, ~1.6GB less memory via no-grad one-hot encoding
• DC_and_CE_loss(soft_dice_kwargs, ce_kwargs, weight_ce=1, weight_dice=1, ignore_label) - Dice + Cross-Entropy (default nnU-Net loss)
• DC_and_BCE_loss(bce_kwargs, soft_dice_kwargs, weight_ce=1, weight_dice=1) - Dice + Binary CE
• DC_and_topk_loss(soft_dice_kwargs, ce_kwargs, weight_ce=1, weight_dice=1) - Dice + TopK

Evaluation metrics (in evaluation/evaluate_predictions.py):

• Computes per-class: Dice, IoU, TP, FP, FN, TN
• compute_tp_fp_fn_tn(mask_ref, mask_pred, ignore_mask) - core confusion matrix
• compute_metrics(reference_file, prediction_file, image_reader_writer, labels_or_regions, ignore_label) - per-file metrics
• compute_metrics_on_folder() / compute_metrics_on_folder_simple() - batch evaluation with multiprocessing

Sliding window inference (in inference/sliding_window_prediction.py):

• compute_steps_for_sliding_window(image_size, tile_size, tile_step_size) - tile_step_size is 0-1 (0.5 = 50% overlap)
• compute_gaussian(tile_size) - Gaussian importance weighting for smooth tile aggregation (center-weighted, no zeros)
• Supports test-time augmentation via mirror axes

Trainer variants (in training/nnUNetTrainer/variants/): Subdirectories for: benchmarking, data_augmentation, loss, lr_schedule, network_architecture, optimizer, sampling, training_length

nbdev Workflow

• All code changes in nbs/*.ipynb
• Run nbdev_prepare to regenerate .py files and run tests
• Never edit fastMONAI/*.py directly

Example Queries

When implementing, fetch relevant docs/code:

"I need to implement a new spatial transform" → Fetch TorchIO spatial transform docs and source

"What's the signature for MONAI's compute_dice?" → Fetch MONAI metrics documentation

"How does nnU-Net handle validation metrics?" → Fetch nnU-Net v2 evaluation code for TP/FP/FN accumulation patterns

"What loss does nnU-Net v2 use by default?" → Fetch compound_losses.py for DC_and_CE_loss (Dice + Cross-Entropy)

"How does nnU-Net v2 do sliding window inference?" → Fetch sliding_window_prediction.py for tile stepping and Gaussian weighting

"What normalization does nnU-Net v2 use for MR images?" → Fetch default_normalization_schemes.py for ZScoreNormalization

"I want to add a new loss function" → Fetch MONAI losses documentation and nnU-Net v2 compound_losses.py

Quick Reference Commands

To check upstream implementations during development:

# TorchIO transform documentation
WebFetch: https://torchio.readthedocs.io/transforms/augmentation.html

# MONAI metric implementation
WebFetch: https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/monai/metrics/meandice.py

# nnU-Net v2 usage guide
WebFetch: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/how_to_use_nnunet.md

# nnU-Net v2 normalization schemes (ZScore, CT, RescaleTo01, etc.)
WebFetch: https://raw.githubusercontent.com/MIC-DKFZ/nnUNet/master/nnunetv2/preprocessing/normalization/default_normalization_schemes.py

# nnU-Net v2 default loss (Dice + CE compound)
WebFetch: https://raw.githubusercontent.com/MIC-DKFZ/nnUNet/master/nnunetv2/training/loss/compound_losses.py

# nnU-Net v2 Dice loss implementation
WebFetch: https://raw.githubusercontent.com/MIC-DKFZ/nnUNet/master/nnunetv2/training/loss/dice.py

# nnU-Net v2 evaluation metrics (Dice, IoU, TP/FP/FN)
WebFetch: https://raw.githubusercontent.com/MIC-DKFZ/nnUNet/master/nnunetv2/evaluation/evaluate_predictions.py

# nnU-Net v2 sliding window inference (Gaussian weighting)
WebFetch: https://raw.githubusercontent.com/MIC-DKFZ/nnUNet/master/nnunetv2/inference/sliding_window_prediction.py

# nnU-Net v2 base trainer (training loop, validation, scheduling)
WebFetch: https://raw.githubusercontent.com/MIC-DKFZ/nnUNet/master/nnunetv2/training/nnUNetTrainer/nnUNetTrainer.py

# nnU-Net v2 extending guide (custom trainers, architectures)
WebFetch: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/extending_nnunet.md