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32 dataset results for MRI

The fastMRI dataset includes two types of MRI scans: knee MRIs and the brain (neuro) MRIs, and containing training, validation, and masked test sets. The deidentified imaging dataset provided by NYU Langone comprises raw k-space data in several sub-dataset groups. Curation of these data are part of an IRB approved study. Raw and DICOM data have been deidentified via conversion to the vendor-neutral ISMRMD format and the RSNA clinical trial processor, respectively. Also, each DICOM image is manually inspected for the presence of any unexpected protected health information (PHI), with spot checking of both metadata and image content. Knee MRI: Data from more than 1,500 fully sampled knee MRIs obtained on 3 and 1.5 Tesla magnets and DICOM images from 10,000 clinical knee MRIs also obtained at 3 or 1.5 Tesla. The raw dataset includes coronal proton density-weighted images with and without fat suppression. The DICOM dataset contains coronal proton density-weighted with and without fat suppr

268 PAPERS • 5 BENCHMARKS

BraTS 2017

The BRATS2017 dataset. It contains 285 brain tumor MRI scans, with four MRI modalities as T1, T1ce, T2, and Flair for each scan. The dataset also provides full masks for brain tumors, with labels for ED, ET, NET/NCR. The segmentation evaluation is based on three tasks: WT, TC and ET segmentation.

72 PAPERS • 1 BENCHMARK

PROMISE12

The PROMISE12 dataset was made available for the MICCAI 2012 prostate segmentation challenge. Magnetic Resonance (MR) images (T2-weighted) of 50 patients with various diseases were acquired at different locations with several MRI vendors and scanning protocols.

72 PAPERS • 1 BENCHMARK

BraTS 2015

The BraTS 2015 dataset is a dataset for brain tumor image segmentation. It consists of 220 high grade gliomas (HGG) and 54 low grade gliomas (LGG) MRIs. The four MRI modalities are T1, T1c, T2, and T2FLAIR. Segmented “ground truth” is provide about four intra-tumoral classes, viz. edema, enhancing tumor, non-enhancing tumor, and necrosis.

66 PAPERS • 1 BENCHMARK

BraTS 2013

BRATS 2013 is a brain tumor segmentation dataset consists of synthetic and real images, where each of them is further divided into high-grade gliomas (HG) and low-grade gliomas (LG). There are 25 patients with both synthetic HG and LG images and 20 patients with real HG and 10 patients with real LG images. For each patient, FLAIR, T1, T2, and post-Gadolinium T1 magnetic resonance (MR) image sequences are available.

35 PAPERS • 2 BENCHMARKS

ADNI

ADNI (Alzheimer's Disease NeuroImaging Initiative)

Alzheimer's Disease Neuroimaging Initiative (ADNI) is a multisite study that aims to improve clinical trials for the prevention and treatment of Alzheimer’s disease (AD).[1] This cooperative study combines expertise and funding from the private and public sector to study subjects with AD, as well as those who may develop AD and controls with no signs of cognitive impairment.[2] Researchers at 63 sites in the US and Canada track the progression of AD in the human brain with neuroimaging, biochemical, and genetic biological markers.[2][3] This knowledge helps to find better clinical trials for the prevention and treatment of AD. ADNI has made a global impact,[4] firstly by developing a set of standardized protocols to allow the comparison of results from multiple centers,[4] and secondly by its data-sharing policy which makes available all at the data without embargo to qualified researchers worldwide.[5] To date, over 1000 scientific publications have used ADNI data.[6] A number of oth

16 PAPERS • 2 BENCHMARKS

BraTS 2016

BRATS 2016 is a brain tumor segmentation dataset. It shares the same training set as BRATS 2015, which consists of 220 HHG and 54 LGG. Its testing dataset consists of 191 cases with unknown grades. Image Source: https://sites.google.com/site/braintumorsegmentation/home/brats_2016

13 PAPERS • NO BENCHMARKS YET

BRATS 2021 (RSNA-ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge 2021)

The RSNA-ASNR-MICCAI BraTS 2021 challenge utilizes multi-institutional pre-operative baseline multi-parametric magnetic resonance imaging (mpMRI) scans, and focuses on the evaluation of state-of-the-art methods for (Task 1) the segmentation of intrinsically heterogeneous brain glioblastoma sub-regions in mpMRI scans. Furthemore, this BraTS 2021 challenge also focuses on the evaluation of (Task 2) classification methods to predict the MGMT promoter methylation status.

10 PAPERS • NO BENCHMARKS YET

ACDC Scribbles

We release expert-made scribble annotations for the medical ACDC dataset 1. The released data must be considered as extending the original ACDC dataset. The ACDC dataset contains cardiac MRI images, paired with hand-made segmentation masks. It is possible to use the segmentation masks provided in the ACDC dataset to evaluate the performance of methods trained using only scribble supervision.

9 PAPERS • 1 BENCHMARK

CHAOS (CHAOS - Combined (CT-MR) Healthy Abdominal Organ Segmentation)

CHAOS challenge aims the segmentation of abdominal organs (liver, kidneys and spleen) from CT and MRI data. ONsite section of the CHAOS was held in The IEEE International Symposium on Biomedical Imaging (ISBI) on April 11, 2019, Venice, ITALY. Online submissions are still welcome!

8 PAPERS • NO BENCHMARKS YET

SKM-TEA

SKM-TEA (Stanford Knee MRI with Multi-Task Evaluation)

The SKM-TEA dataset pairs raw quantitative knee MRI (qMRI) data, image data, and dense labels of tissues and pathology for end-to-end exploration and evaluation of the MR imaging pipeline. This 1.6TB dataset consists of raw-data measurements of ~25,000 slices (155 patients) of anonymized patient knee MRI scans, the corresponding scanner-generated DICOM images, manual segmentations of four tissues, and bounding box annotations for sixteen clinically relevant pathologies.

7 PAPERS • NO BENCHMARKS YET

ATLAS v2.0 (Anatomical Tracings of Lesions After Stroke Dataset version 2.0)

Accurate lesion segmentation is critical in stroke rehabilitation research for the quantification of lesion burden and accurate image processing. Current automated lesion segmentation methods for T1-weighted (T1w) MRIs, commonly used in rehabilitation research, lack accuracy and reliability. Manual segmentation remains the gold standard, but it is time-consuming, subjective, and requires significant neuroanatomical expertise. However, many methods developed with ATLAS v1.2 report low accuracy, are not publicly accessible or are improperly validated, limiting their utility to the field. Here we present ATLAS v2.0 (N=1271), a larger dataset of T1w stroke MRIs and manually segmented lesion masks that includes training (public. n=655), test (masks hidden, n=300), and generalizability (completely hidden, n=316) data. Algorithm development using this larger sample should lead to more robust solutions, and the hidden test and generalizability datasets allow for unbiased performance evaluation

6 PAPERS • 1 BENCHMARK

BraTS 2014

BRATS 2014 is a brain tumor segmentation dataset.

5 PAPERS • 1 BENCHMARK

Duke Breast Cancer MRI (Dynamic contrast-enhanced magnetic resonance images of breast cancer patients with tumor locations)

Breast MRI scans of 922 cancer patients from Duke University, with tumor bounding box annotations, clinical, imaging, and many other features, and more.

5 PAPERS • NO BENCHMARKS YET

HaN-Seg (The Head and Neck Organ-at-Risk CT & MR Segmentation Challenge)

Cancer in the region of the head and neck (HaN) is one of the most prominent cancers, for which radiotherapy represents an important treatment modality that aims to deliver a high radiation dose to the targeted cancerous cells while sparing the nearby healthy organs-at-risk (OARs). A precise three-dimensional spatial description, i.e. segmentation, of the target volumes as well as OARs is required for optimal radiation dose distribution calculation, which is primarily performed using computed tomography (CT) images. However, the HaN region contains many OARs that are poorly visible in CT, but better visible in magnetic resonance (MR) images. Although attempts have been made towards the segmentation of OARs from MR images, so far there has been no evaluation of the impact the combined analysis of CT and MR images has on the segmentation of OARs in the HaN region. The Head and Neck Organ-at-Risk Multi-Modal Segmentation Challenge aims to promote the development of new and application of

5 PAPERS • NO BENCHMARKS YET

OASIS-1 (Open Access Series of Imaging Studies)

The Open Access Series of Imaging Studies (OASIS) is a project aimed at making neuroimaging data sets of the brain freely available to the scientific community. By compiling and freely distributing neuroimaging data sets, we hope to facilitate future discoveries in basic and clinical neuroscience.

5 PAPERS • NO BENCHMARKS YET

Sunnybrook Cardiac Data

The Sunnybrook Cardiac Data (SCD), also known as the 2009 Cardiac MR Left Ventricle Segmentation Challenge data, consist of 45 cine-MRI images from a mixed of patients and pathologies: healthy, hypertrophy, heart failure with infarction and heart failure without infarction. Subset of this data set was first used in the automated myocardium segmentation challenge from short-axis MRI, held by a MICCAI workshop in 2009. The whole complete data set is now available in the CAP database with public domain license.

5 PAPERS • NO BENCHMARKS YET

ABIDE (Autism Brain Imaging Data Exchange)

Autism spectrum disorder (ASD) is characterized by qualitative impairment in social reciprocity, and by repetitive, restricted, and stereotyped behaviors/interests. Previously considered rare, ASD is now recognized to occur in more than 1% of children. Despite continuing research advances, their pace and clinical impact have not kept up with the urgency to identify ways of determining the diagnosis at earlier ages, selecting optimal treatments, and predicting outcomes. For the most part this is due to the complexity and heterogeneity of ASD. To face these challenges, large-scale samples are essential, but single laboratories cannot obtain sufficiently large datasets to reveal the brain mechanisms underlying ASD. In response, the Autism Brain Imaging Data Exchange (ABIDE) initiative has aggregated functional and structural brain imaging data collected from laboratories around the world to accelerate our understanding of the neural bases of autism. With the ultimate goal of facilitating

3 PAPERS • NO BENCHMARKS YET

EPISURG

EPISURG (EPISURG: a dataset of postoperative MRI for quantitative analysis of resection neurosurgery for refractory epilepsy)

EPISURG is a clinical dataset of $T_1$-weighted magnetic resonance images (MRI) from 430 epileptic patients who underwent resective brain surgery at the National Hospital of Neurology and Neurosurgery (Queen Square, London, United Kingdom) between 1990 and 2018.

2 PAPERS • NO BENCHMARKS YET

IBC

IBC (Individual Brain Charting)

The Individual Brain Charting (IBC) project aims at providing a new generation of functional-brain atlases. To map cognitive mechanisms in a fine scale, task-fMRI data at high-spatial-resolution are being acquired on a fixed cohort of 12 participants, while performing many different tasks. These data—free from both inter-subject and inter-site variability—are publicly available as means to support the investigation of functional segregation and connectivity as well as individual variability with a view to establishing a better link between brain systems and behavior.

2 PAPERS • NO BENCHMARKS YET

TCIA Brain-Tumor-Progression

This collection includes datasets from 20 subjects with primary newly diagnosed glioblastoma who were treated with surgery and standard concomitant chemo-radiation therapy (CRT) followed by adjuvant chemotherapy. Two MRI exams are included for each patient: within 90 days following CRT completion and at progression (determined clinically, and based on a combination of clinical performance and/or imaging findings, and punctuated by a change in treatment or intervention). All image sets are in DICOM format and contain T1w (pre and post-contrast agent), FLAIR, T2w, ADC, normalized cerebral blood flow, normalized relative cerebral blood volume, standardized relative cerebral blood volume, and binary tumor masks (generated using T1w images). The perfusion images were generated from dynamic susceptibility contrast (GRE-EPI DSC) imaging following a preload of contrast agent. All of the series are co-registered with the T1+C images. The intent of this dataset is for assessing deep learnin

2 PAPERS • NO BENCHMARKS YET

Tc1 Mouse cerebellum atlas (Tc1 Mouse cerebellum atlas with Purkinje layer segmentation)

This mouse cerebellar atlas can be used for mouse cerebellar morphometry.

2 PAPERS • NO BENCHMARKS YET

Algonauts 2023

The Algonauts 2023 Challenge focuses on predicting responses in the human brain as participants perceive complex natural visual scenes. Through collaboration with the Natural Scenes Dataset (NSD) team, the Challenge runs on the largest suitable brain dataset available, opening new venues for data-hungry modeling.

1 PAPER • NO BENCHMARKS YET

BreastDICOM4 ([MIMBCD-UI] UTA4: Medical Imaging DICOM Files Dataset)

Several datasets are fostering innovation in higher-level functions for everyone, everywhere. By providing this repository, we hope to encourage the research community to focus on hard problems. In this repository, we present our medical imaging DICOM files of patients from our User Tests and Analysis 4 (UTA4) study. Here, we provide a dataset of the used medical images during the UTA4 tasks. This repository and respective dataset should be paired with the dataset-uta4-rates repository dataset. Work and results are published on a top Human-Computer Interaction (HCI) conference named AVI 2020 (page). Results were analyzed and interpreted on our Statistical Analysis charts. The user tests were made in clinical institutions, where clinicians diagnose several patients for a Single-Modality vs Multi-Modality comparison. For example, in these tests, we used both prototype-single-modality and prototype-multi-modality repositories for the comparison. On the same hand, the hereby dataset repres

1 PAPER • 1 BENCHMARK

CEREBRUM-7T (Fast and Fully-volumetric Brain Segmentation of 7 Tesla MR Volumes)

Ultra-high field MRI enables sub-millimetre resolution imaging of human brain, allowing to disentangle complex functional circuits across different cortical depths. Segmentation, meant as the partition of MR brain images in multiple anatomical classes, is an essential step in many functional and structural neuroimaging studies. In this work, we design and test CEREBRUM-7T, an optimised end-to-end CNN architecture, that allows to segment a whole 7T T1w MRI brain volume at once, without the need of partitioning it into 2D or 3D tiles. Despite deep learning (DL) methods are recently starting to emerge in 3T literature, to the best of our knowledge, CEREBRUM-7T is the first example of DL architecture directly applied on 7T data. Training is performed in a weakly supervised fashion, since it exploits a ground-truth (GT) with errors. The generated model is able to produce accurate multi-structure segmentation masks on six different classes, in only few seconds. In the experimental part, we s

1 PAPER • NO BENCHMARKS YET

Cam-CAN (Cambridge Centre for Ageing and Neuroscience dataset)

The Cambridge Centre for Ageing and Neuroscience (Cam-CAN) is a large-scale collaborative research project at the University of Cambridge, launched in October 2010, with substantial initial funding from the Biotechnology and Biological Sciences Research Council (BBSRC), followed by support from the Medical Research Council (MRC) Cognition & Brain Sciences Unit (CBU) and the European Union Horizon 2020 LifeBrain project. The Cam-CAN project uses epidemiological, cognitive, and neuroimaging data to understand how individuals can best retain cognitive abilities into old age.

1 PAPER • NO BENCHMARKS YET

Deep Deep Learning With BART (Trained Weights and Example Data)

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1 PAPER • NO BENCHMARKS YET

LPBA40

LPBA40 (LONI Probabilistic Brain Atlas)

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1 PAPER • NO BENCHMARKS YET

Multi-template MRI mouse brain atlas (Multi-template MRI mouse brain atlas for both in vivo and ex vivo analysis)

Mouse Brain MRI atlas (both in-vivo and ex-vivo) (repository relocated from the original webpage)

1 PAPER • NO BENCHMARKS YET

SR-Reg (SynthRAD Registration)

SR-Reg is a brain MR-CT registration dataset, deriving from SynthRAD 2023 (https://synthrad2023.grand-challenge.org/). This dataset contains 180 subjects preprocessed images, and each subject comprises a brain MR image and a brain CT image with corresponding segmentation label. SR-Reg is first introduced in MambaMorph (https://arxiv.org/abs/2401.13934).

1 PAPER • 1 BENCHMARK

Symbrain

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1 PAPER • NO BENCHMARKS YET

Volumetric CMR Cartesian Datasets (Free-running self-gated 3D cine, 4D Flow and stress 4D Flow Undersampled Datasets)

Datasets at https://zenodo.org/record/8105485 for Motion Robust CMR Reconstruction Code in https://github.com/syedmurtazaarshad/motion-robust-CMR

1 PAPER • NO BENCHMARKS YET