README.md

---
title: MR-RATE-atlas Dataset
license: cc-by-nc-sa-4.0
task_categories:
- image-to-text
- text-to-image
- image-classification
- question-answering
- visual-question-answering
- zero-shot-classification
language:
- en 
tags:
- brain-mri
- radiology
- science
- huggingscience
- 3d-medical-imaging
- medical
- mr-rate
- multimodal
- vision-language
- healthcare
- diagnostic-imaging
- computer-vision
- foundation-model
size_categories:
- 10K<n<100K
pretty_name: "MR-RATE-atlas: Atlas-Registered Brain MRI Volumes"
extra_gated_prompt: >
  ## Terms and Conditions for Using the MR-RATE Dataset
  
  **1. Acceptance of Terms**
  Accessing and using the MR-RATE dataset implies your agreement to these terms
  and conditions. If you disagree with any part, please refrain from using the
  dataset.


  **2. Permitted Use**

  - The dataset is intended solely for academic, research, and educational
  purposes.

  - Any commercial exploitation of the dataset without prior permission is
  strictly forbidden.

  - You must adhere to all relevant laws, regulations, and research ethics,
  including data privacy and protection standards.


  **3. Data Protection and Privacy**

  - Acknowledge the presence of sensitive information within the dataset and
  commit to maintaining data confidentiality.

  - Direct attempts to re-identify individuals from the dataset are prohibited.

  - Ensure compliance with data protection laws such as GDPR and HIPAA.


  **4. Attribution**

  - Cite the dataset and acknowledge the providers in any publications resulting
  from its use.

  - Claims of ownership or exclusive rights over the dataset or derivatives are
  not permitted.


  **5. Redistribution**

  - Redistribution of the dataset or any portion thereof is not allowed.

  - Sharing derived data must respect the privacy and confidentiality terms set
  forth.


  **6. Disclaimer**

  The dataset is provided "as is" without warranty of any kind, either expressed
  or implied, including but not limited to the accuracy or completeness of the
  data.


  **7. Limitation of Liability**

  Under no circumstances will the dataset providers be liable for any claims or
  damages resulting from your use of the dataset.


  **8. Access Revocation**

  Violation of these terms may result in the termination of your access to the
  dataset.


  **9. Amendments**

  The terms and conditions may be updated at any time; continued use of the
  dataset signifies acceptance of the new terms.


  **10. Governing Law**

  These terms are governed by the laws of the location of the dataset providers,
  excluding conflict of law rules.


  **Consent:**

  Accessing and using the MR-RATE dataset signifies your acknowledgment and
  agreement to these terms and conditions.
extra_gated_fields:
  First Name: text
  Last Name: text
  Institution: text
  Role: text
  Email: text
  I have read and agree with Terms and Conditions for using the MR-RATE dataset: checkbox
---
<p align="center">
  <span style="font-size: 24px; font-weight: 700;">
    MR-RATE: A Vision-Language Foundation Model and Dataset for Magnetic Resonance Imaging
  </span>
</p>
<p align="center">
  &nbsp; | &nbsp; <strong>Paper</strong> (Coming soon) &nbsp; | &nbsp;
  <a href="https://github.com/forithmus/MR-RATE">GitHub</a> &nbsp; | &nbsp;
  <a href="https://huggingface.co/datasets/Forithmus/MR-RATE/blob/main/README.md#dataset-organization--getting-started">Dataset Access</a> &nbsp; | &nbsp;
  <a href="https://mrrate.forithmus.com/">Dataset Explorer</a> &nbsp; | &nbsp;
  <strong>Model Weights</strong> (Coming soon) &nbsp; | &nbsp;
</p>

This is the **MR-RATE-atlas** repository, part of the **MR-RATE** dataset release. It contains atlas-registered brain MRI volumes in which all imaging sequences within each study have been spatially normalized to a standard atlas-space. For full dataset details, native-space MRI volumes, radiology reports, metadata, and data splits, please refer to the [MR-RATE](https://huggingface.co/datasets/Forithmus/MR-RATE) repository. To explore, download, and work with the dataset see **[Dataset Organization & Getting Started](https://huggingface.co/datasets/Forithmus/MR-RATE/blob/main/README.md#dataset-organization--getting-started)**.

# Atlas-Registered Brain MRI Volumes

Within each study, the T1-weighted brain MRI volume serving as the center modality is rigidly registered to the [MNI152 (ICBM 2009c Nonlinear Symmetric)](https://nist.mni.mcgill.ca/icbm-152-nonlinear-atlases-2009/) atlas using [ANTs](https://github.com/antsx/ants). The native-space moving modality brain MRI volumes, and the brain masks and defacing masks of center modalities from [MR-RATE](https://huggingface.co/datasets/Forithmus/MR-RATE) repository are then transformed to atlas-space by composing the native-to-center and center-to-atlas registration transforms, bringing all sequences of a given study into a standardized coordinate space that enables group-level analyses and cross-patient comparisons.

This repository provides:
- **Atlas-registered center modalities** (in NIfTI format) — All T1-weighted center modality brain MRI volumes, and corresponding brain masks and defacing masks warped to atlas-space
- **Atlas-registered moving modalities** (in NIfTI format) — All moving modality brain MRI volumes transformed to atlas-space
- **Registration transforms** (in .mat format) — The ANTs registration transform files mapping each center modality to the atlas, enabling users to apply them in their custom workflows

Study folders are zipped to comply with Hugging Face's per-repository file count limits.

---

# Citing Us
When using this dataset, please consider citing the following related papers:

```
Coming soon
```

# Ethical Approval
This study was approved by the Clinical Research Ethics Committee at Istanbul Medipol University (E-10840098-772.02-6841, 27/10/2023). All MRI volumes, metadata, and radiology reports were fully anonymized prior to analysis to protect patient privacy.

# License
We are committed to fostering innovation and collaboration in the research community. To this end, all elements of the MR-RATE dataset are released under a **[Creative Commons Attribution–NonCommercial–ShareAlike (CC BY-NC-SA)](https://creativecommons.org/licenses/by-nc-sa/4.0/)** license.

This licensing framework ensures that our contributions can be freely used for non-commercial research purposes, while also encouraging contributions and modifications, provided that the original work is properly cited and any derivative works are shared under similar terms.

For commercial inquiries related to MR-RATE, please contact: contact@forithmus.com.