hyperresashs 1.0.8

Isotropic segmentation pipeline for MTL subregions from multi-modality 3T MRI

HyperResASHS

HyperResASHS is a deep learning pipeline for isotropic segmentation of medial temporal lobe (MTL) subregions from multi-modality 3T MRI (T1w and T2w). This repository implements the method described in our paper for achieving high-resolution, isotropic segmentation of brain structures.

Overview

This project addresses the challenge of segmenting MTL subregions from anisotropic MRI data by:

1. Building an isotropic atlas using Implicit Neural Representations (INR)
2. Training a multi-modality segmentation model with nnU-Net
3. Performing inference on test data with automatic preprocessing

The pipeline handles the entire workflow from raw multi-modality MRI images to final segmentation results, including registration, ROI extraction, upsampling, and model inference.

Requirements

• NVidia GPU is needed to run training and inference. It is possible to run inference on CPU but runtimes will be over an hour per case, vs. ~3 minutes on GPU.
• A Python (version 3.10 or greater) environment with conda package manager and is recommended

Easy Setup (Most Users)

Follow these steps to set up the repository in a fresh environment:

1. Create a Conda Environment

Create a new conda environment with Python 3.10 or higher:

conda create -n hyperresashs python=3.10
conda activate hyperresashs

An alternative to using conda is to create a Python virtual environment

cd /my/project/path
python -v env .venv
source .venv/bin/activate

2. Install hyperresashs from PyPi

Install the package and all dependencies

pip install hyperresashs

Check that the install was successful

hrashs check

The command should report that HyperResASHS was successfully installed and print the software version. If you see errors/warnings related to PyTorch and CUDA, please follow more detailed instructions for installing PyTorch under Advanced Setup below.

Advanced Setup (Developers)

Follow these steps to set up the repository in a fresh environment:

1. Create a Conda Environment

Create a new conda environment with Python 3.10 or higher:

conda create -n hyperresashs python=3.10
conda activate hyperresashs

2. Clone the Repository

Clone the repository with submodules:

git clone --recursive https://github.com/pyushkevich/HyperResASHS.git
cd HyperResASHS

If you've already cloned without submodules, initialize them with:

git submodule update --init --recursive

3. Install Python Dependencies

Important: PyTorch version compatibility is critical. This pipeline requires PyTorch 2.5.x (tested with 2.5.1). Newer versions (e.g., 2.9) may cause compatibility issues.

For optimal performance, you should install PyTorch library optimized for your CUDA version. To check your CUDA version, type

nvidia-smi | grep "CUDA Version"

The output will be like this. If you get an error, then CUDA is probably not configured on your machine.

| NVIDIA-SMI 535.288.01             Driver Version: 535.288.01   CUDA Version: 12.2     |

Then enter the following command, with cu118 changed to match your cuda version (e.g., cu122):

# For CUDA 11.8:
pip install torch==2.5.1 torchvision==0.20.1 torchaudio==2.5.1 --index-url https://download.pytorch.org/whl/cu118

Then install the package and remaining dependencies:

# Then install the package and remaining dependencies
pip install -e .

6. Verify Installation

Verify that the package and dependencies are installed correctly:

hrashs check

Basic Usage

HyperResASHS provides a command-line interface for running segmentation on new subjects using pre-trained models.

1. List Available Models

View all pre-trained models available for download:

hrashs list

This displays model IDs, names, and brief descriptions of each available model.

2. View Model Details

Get detailed information about a specific model including required inputs and expected outputs:

hrashs desc <model_id>

Example:

hrashs desc HSG_Body_Atlas

3. Run Segmentation

Run segmentation on your subject data:

hrashs run -a <model_id> -g <t1_image> -f <t2_image> -w <workdir>

Required arguments:

• -a, --atlas: Model ID or path to atlas config file
• -g, --t1: Path to T1-weighted (MPRAGE) image
• -f, --t2: Path to T2-weighted (TSE) image
• -w, --workdir: Output directory for results

Optional arguments:

• -I, --subject: Subject ID, which will be prefixed to all output filenames
• -t, --threads: Number of parallel threads for registration, etc. [default: 1]
• --device: Device for computation ("cuda" or "cpu") [default: auto]
• -N, --no-overwrite: Do not overwrite existing results
• -L, --no-links: Copy files instead of creating symlinks
• -T, --tidy: Reduce intermediate files
• -k, --disable-ssl-verification: Disable SSL verification for Hugging Face

Example:

hrashs run -a HSG_Body_Atlas -g mprage.nii.gz -f tse.nii.gz -I sub01 -w ./output -t 4

Outputs: Segmentation results are saved in the final subfolder of the output directory. Two types of images are generated:

• [subject]_tse_patch_hyperres_seg_[side].nii.gz: These are HyperResASHS segmentations with nearly isotropic resolution (e.g., 0.4x0.4x0.4mm^3). We recommend using these images for volumetry, thickness computation, running CRASHS, etc.
• [subject]_tse_native_seg_[side].nii.gz: These segmentations have been downsampled to original T2-MRI space. They can be used for visualization or computing similarity metrics with manual segmentations. However, these segmentations suffer from step edge artifacts when the T2-MRI is anisotropic.
• [subject]_hyperres_volumes.csv: A CSV file with subfield volumes (computed from hyper-resolution segmentations).

QC Images: Registration and segmentation QC images in .png format are placed in the qc subfolder of the output directory.

Training

Train a custom HyperResASHS model on your own dataset:

hrashs train -c <config> -m <manifest> -l <labels> -w <workdir>

Required arguments:

• -c, --config: Path to training configuration YAML file (see format below)
• -m, --manifest: Path to manifest CSV describing the training data
• -l, --labels: Path to ITK-SNAP label description file
• -w, --workdir: Output directory for training artifacts

Optional arguments:

• -x, --xval: Cross-validation fold file (if not provided, random 5-fold split is used)
• -s, --stage: Run specific stage(s): 1 (preprocess), 2 (INR), 3 (nnU-Net prep), 4 (nnU-Net train), or ranges like 1-3
• -F, --filter: Regex to filter subjects/folds (stage-dependent)
• -R, --inr-random-seed: Random seed for INR optimization
• --inr-batch-size: INR batch size [default: 2000]
• --inr-epochs: INR training epochs [default: 60]
• -t, --threads, --device, -N, -L, -T, -k: Same as run command

Example:

hrashs train -c atlas.yaml -m manifest.csv -l labels.txt -w ./training -s 1-2 -t 8

Configuration File Format (-c)

YAML file with atlas metadata and training parameters.

metadata:
  id: 'MyAtlas'
  name: 'My Custom Atlas'
  version: '1.0.0'
config:
  EXP_NUM: 401                                  # Unique experiment number
  MODEL_NAME: 'IsotropicSeg'                    # Model name
  TRAINER: 'ModAugPartialCoverageUNetTrainer'   # nnU-Net trainer class
  CONDITION: 'in_vivo'                          # Condition identifier
  UPSAMPLING_METHOD: 'INRUpsampling'
  SIDES:
    - left
    - right

The following parameters are included in the config:

EXP_NUM: A unique numeric key for this experiment.

TRAINER: Name of the nnU-Net class used for training. This is important at it determines the type of augmentation used. ModAugUNetTrainer is the trainer with modality augmentation (modalities are occasionally excluded during training to force the model to learn from all available modalities). ModAugPartialCoverageUNetTrainer offers modality augmentation plus augmentation for partial coverage that may be more robust for slab TSE images. Other trainers provided by nnU-Net or included in the hyperresashs/submodules/nnUNet/nnunetv2/training/nnUNetTrainer/variants/data_augmentation folder can also be specified.

UPSAMPLING_METHOD: How images and segmentations are upsampled during training. INRUpsampling uses implicit neural representation to upsample the segmentations to isotropic or nearly isotropic resolution during training. This is recommended for highly anisotropic TSE scans and manual segmentations. Other options are None for no upsampling and GreedyUpsampling for faster upsampling based on Gaussian smoothing and voting (not recommended).

TARGET_SPACING: Specifies the resolution to which images should be upsampled when using INRUpsampling. By default (value 0.0), resolution is determined based on the TSE image, making the image isotropic or nearly isotropic. For example, image with 0.4x0.5x2.0 resolution would be upsampled to 0.4x0.5x0.4. You can also specify a target resolution here, either as a vector 0.4x0.4x0.4 or as the desired dimension 0.4.

SIDES: When left and right target structures are segmented using separately trained nnU-Net networks (e.g., medial temporal lobe), this should be a list containing left, right. For structures that do not separate by hemisphere (e.g., brainstem), this can be mid.

MODEL_NAME: Name of the model used for the segmentation. Currently only IsotropicSeg is supported.

CONDITION: Should be in_vivo

Manifest File Format (-m)

CSV file listing training cases. Paths can be absolute or relative to the manifest file:

id,date,mprage,tse,seg_left,seg_right
subj01,2024-01-15,subj01/mprage.nii.gz,subj01/tse.nii.gz,subj01/seg_left.nii.gz,subj01/seg_right.nii.gz
subj02,,subj02/mprage.nii.gz,subj02/tse.nii.gz,subj02/seg_left.nii.gz,subj02/seg_right.nii.gz

Required columns: id, mprage, tse, seg_left, seg_right. The date column is optional.

Label File Format (-l)

ITK-SNAP label description file format:

# IDX   -R-  -G-  -B-  -A--  VIS MSH  LABEL
   0     0    0    0    0    0   0    "Clear Label"
   1   255    0    0    1    1   1    "CA1"
   2     0  255    0    1    1   1    "CA2"

Cross-Validation File Format (-x)

Optional text file where each line lists subject IDs for one held-out fold (space-separated):

subj01 subj02 subj03
subj04 subj05 subj06
subj07 subj08 subj09

Output Structure

workdir/
├── preproc/           # Preprocessed images per subject
├── inr_training/      # INR training data and outputs
├── nnunet_training/   # nnU-Net datasets and trained models
└── final/             # Final trained atlas ready for deployment

For detailed configuration information, see Configuration Guide.

Citation

If you use this code in your research, please cite our paper:

@article{hyperresashs2024,
  title={HyperResASHS: Isotropic Segmentation of MTL Subregions from Multi-modality 3T MRI},
  author={[Authors]},
  journal={arXiv preprint arXiv:2508.17171},
  year={2024},
  url={https://doi.org/10.48550/arXiv.2508.17171}
}

Changelog

01/14/2026

• Replaced trim_neck.sh shell script with Python implementation using picsl_c3d package
• Removed ITK-SNAP installation requirement (no longer needed)
• Updated multi_contrast_inr submodule to latest version
• Modified --config_id argument to accept both integer ID and full file path
• Added config validation checks: ID consistency, conflict detection, and nnUNet dataset existence
• Made FILE_NAME_CONFIG optional with automatic defaults based on stage (test vs. other stages)
• Renamed scripts/ folder to shell/ for better clarity
• Added optional --subject_id argument for test stage to test specific subjects
• Updated .gitignore to exclude generated config and script files while keeping template files tracked
• Fixed config validation to skip checks when stage is test

01/07/2026

• Added requirements.txt and setup.py with pinned package versions for reproducible installation
• Added nnU-Net environment variables setup instructions
• Added Python stages for INR upsampling (stage = run_inr) and nnU-Net training (stage = train)
• Created comprehensive documentation in docs/ folder:
  • Configuration guide with training and test config details
  • INR upsampling shell script guide
  • nnU-Net training shell script guide
• Updated README to reference documentation files for better organization
• Added trim_neck.sh script for neck trimming
• Updated testing documentation with config_test details and test data structure
• Changed default pipeline stage from prepare_inr to prepare

01/04/2026

• Refactored pipeline to support linear execution order
• Added separate prepare stage for patch data preparation
• Simplified execute() method in preprocessing to remove conditional checks
• Updated pipeline documentation to reflect linear execution flow
• Added .gitignore to exclude Python cache files and build artifacts

12/24/2025

• Added INR and modified nnUNet as git submodules
• Added INR preparation module with config generation
• Added INR upsampling script template and generation
• Added nnUNet training script template and generation
• Updated README with submodule setup and pipeline documentation

12/22/2025

• Updated README.md with comprehensive documentation
• Added data structure documentation slots for atlas and test data

11/20/2025

• Added main pipeline of preprocessing

10/27/2025

• Initial release of isotropic segmentation pipeline for MTL subregions
• Support for 3T-T2w and 3T-T1w multi-modality MRI

Contact

For questions or support, please open an issue or contact [e-mail].