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.

OASIS-1 set consists of a cross-sectional collection of 416 subjects aged 18 to 96. For each subject, 3 or 4 individual T1-weighted MRI scans obtained in single scan sessions are included. The subjects are all right-handed and include both men and women. 100 of the included subjects over the age of 60 have been clinically diagnosed with very mild to moderate Alzheimer’s disease (AD). Additionally, a reliability data set is included containing 20 nondemented subjects imaged on a subsequent visit within 90 days of their initial session.

The dataset used is the OASIS MRI dataset (https://sites.wustl.edu/oasisbrains/), which consists of 80,000 brain MRI images. The images have been divided into four classes based on Alzheimer's progression. The dataset aims to provide a valuable resource for analyzing and detecting early signs of Alzheimer's disease.

To make the dataset accessible, the original .img and .hdr files were converted into Nifti format (.nii) using FSL (FMRIB Software Library). The converted MRI images of 461 patients have been uploaded to a GitHub repository, which can be accessed in multiple parts.

For the neural network training, 2D images were used as input. The brain images were sliced along the z-axis into 256 pieces, and slices ranging from 100 to 160 were selected from each patient. This approach resulted in a comprehensive dataset for analysis.

Patient classification was performed based on the provided metadata and Clinical Dementia Rating (CDR) values, resulting in four classes: demented, very mild demented, mild demented, and non-demented. These classes enable the detection and study of different stages of Alzheimer's disease progression.

During the dataset preparation, the .nii MRI scans were converted to .jpg files. Although this conversion presented some challenges, the files were successfully processed using appropriate tools. The resulting dataset size is 1.3 GB.

With this comprehensive dataset, the project aims to explore various neural network models and achieve optimal results in Alzheimer's disease detection and analysis.

Acknowledgments: “Data were provided 1-12 by OASIS-1: Cross-Sectional: Principal Investigators: D. Marcus, R, Buckner, J, Csernansky J. Morris; P50 AG05681, P01 AG03991, P01 AG026276, R01 AG021910, P20 MH071616, U24 RR021382”

Citation: OASIS-1: Cross-Sectional: https://doi.org/10.1162/jocn.2007.19.9.1498

If you are looking for processed NifTi image version of this dataset please click here

OASIS-3 and OASIS-4 are the latest releases in the Open Access Series of Imaging Studies (OASIS) that is aimed at making neuroimaging datasets freely available to the scientific community. By compiling and freely distributing this multimodal dataset generated by the Knight ADRC and its affiliated studies, we hope to facilitate future discoveries in basic and clinical neuroscience. OASIS-4 contains MR, clinical, cognitive, and biomarker data for 663 individuals aged 21 to 94 that presented with memory complaints. This is a unique dataset and not an update to the OASIS-3 Longitudinal Multimodal Neuroimaging dataset.

Project aimed at making neuroimaging data sets of brain freely available to scientific community. By compiling and freely distributing neuroimaging data sets, future discoveries in basic and clinical neuroscience are facilitated.

Context:

The Open Access Series of Imaging Studies (OASIS) is a project aimed at making MRI data sets of the brain freely available to the scientific community. By compiling and freely distributing MRI data sets, we hope to facilitate future discoveries in basic and clinical neuroscience. OASIS is made available by the Washington University Alzheimer’s Disease Research Center, Dr. Randy Buckner at the Howard Hughes Medical Institute (HHMI)( at Harvard University, the Neuroinformatics Research Group (NRG) at Washington University School of Medicine, and the Biomedical Informatics Research Network (BIRN).

Content:

• Cross-sectional MRI Data in Young, Middle Aged, Nondemented and Demented Older Adults: This set consists of a cross-sectional collection of 416 subjects aged 18 to 96. For each subject, 3 or 4 individual T1-weighted MRI scans obtained in single scan sessions are included. The subjects are all right-handed and include both men and women. 100 of the included subjects over the age of 60 have been clinically diagnosed with very mild to moderate Alzheimer’s disease (AD). Additionally, a reliability data set is included containing 20 nondemented subjects imaged on a subsequent visit within 90 days of their initial session.
• Longitudinal MRI Data in Nondemented and Demented Older Adults: This set consists of a longitudinal collection of 150 subjects aged 60 to 96. Each subject was scanned on two or more visits, separated by at least one year for a total of 373 imaging sessions. For each subject, 3 or 4 individual T1-weighted MRI scans obtained in single scan sessions are included. The subjects are all right-handed and include both men and women. 72 of the subjects were characterized as nondemented throughout the study. 64 of the included subjects were characterized as demented at the time of their initial visits and remained so for subsequent scans, including 51 individuals with mild to moderate Alzheimer’s disease. Another 14 subjects were characterized as nondemented at the time of their initial visit and were subsequently characterized as demented at a later visit.

Acknowledgements:

When publishing findings that benefit from OASIS data, please include the following grant numbers in the acknowledgements section and in the associated Pubmed Central submission: P50 AG05681, P01 AG03991, R01 AG021910, P20 MH071616, U24 RR0213

Inspiration:

Can you predict dementia? Alzheimer’s?

Analysis of ‘MRI and Alzheimers’ provided by Analyst-2 (analyst-2.ai), based on source dataset retrieved from https://www.kaggle.com/jboysen/mri-and-alzheimers on 28 January 2022.

--- Dataset description provided by original source is as follows ---

Context:

The Open Access Series of Imaging Studies (OASIS) is a project aimed at making MRI data sets of the brain freely available to the scientific community. By compiling and freely distributing MRI data sets, we hope to facilitate future discoveries in basic and clinical neuroscience. OASIS is made available by the Washington University Alzheimer’s Disease Research Center, Dr. Randy Buckner at the Howard Hughes Medical Institute (HHMI)( at Harvard University, the Neuroinformatics Research Group (NRG) at Washington University School of Medicine, and the Biomedical Informatics Research Network (BIRN).

Content:

• Cross-sectional MRI Data in Young, Middle Aged, Nondemented and Demented Older Adults: This set consists of a cross-sectional collection of 416 subjects aged 18 to 96. For each subject, 3 or 4 individual T1-weighted MRI scans obtained in single scan sessions are included. The subjects are all right-handed and include both men and women. 100 of the included subjects over the age of 60 have been clinically diagnosed with very mild to moderate Alzheimer’s disease (AD). Additionally, a reliability data set is included containing 20 nondemented subjects imaged on a subsequent visit within 90 days of their initial session.
• Longitudinal MRI Data in Nondemented and Demented Older Adults: This set consists of a longitudinal collection of 150 subjects aged 60 to 96. Each subject was scanned on two or more visits, separated by at least one year for a total of 373 imaging sessions. For each subject, 3 or 4 individual T1-weighted MRI scans obtained in single scan sessions are included. The subjects are all right-handed and include both men and women. 72 of the subjects were characterized as nondemented throughout the study. 64 of the included subjects were characterized as demented at the time of their initial visits and remained so for subsequent scans, including 51 individuals with mild to moderate Alzheimer’s disease. Another 14 subjects were characterized as nondemented at the time of their initial visit and were subsequently characterized as demented at a later visit.

Acknowledgements:

When publishing findings that benefit from OASIS data, please include the following grant numbers in the acknowledgements section and in the associated Pubmed Central submission: P50 AG05681, P01 AG03991, R01 AG021910, P20 MH071616, U24 RR0213

Inspiration:

Can you predict dementia? Alzheimer’s?

--- Original source retains full ownership of the source dataset ---

Link Function: information

A free collection of MRI brain images for testing segmentation algorithms. It is available for download to assess the accuracy, reproducibility and sensitivity of MRI segmentation software. It includes data from infants and adults as well as patients with Alzheimer's disease.

The Mindboggle-101 dataset is part of the Mindboggle project (http://mindboggle.info) and includes anatomically labeled brain surfaces and volumes derived from magnetic resonance images of 101 healthy individuals. The manually edited cortical labels follow sulcus landmarks according to the Desikan-Killiany-Tourville (DKT) labeling protocol: "101 labeled brain images and a consistent human cortical labeling protocol" Arno Klein, Jason Tourville. Frontiers in Brain Imaging Methods. 6:171. DOI: 10.3389/fnins.2012.00171 Data and License All labeled data, including nifti volumes (nii), vtk surfaces (vtk), and FreeSurfer files (mgh, etc.) for each scanned "GROUP" (OASIS-TRT-20, NKI-TRT-20, NKI-RS-22, MMRR-21, HLN-12, etc.) are licensed under a Creative Commons License. These brains are in their original space as well as affine-registered to "MNI152space": [GROUP]_volumes.tar.gz SurfaceLabels_[GROUP].tar.gz The manually labeled subcortical portions of the "WholeBrain" OASIS-TRT-20 labels are licensed under a similar Creative Commons License: WholeBrain_VolumeLabels_OASIS-TRT-20.tar.gz WholeBrain_VolumeLabels_OASIS-TRT-20_MNI152space.tar.gz The following code and documentation files are also included: CHANGELOG.txt: log of changes code_prep_WholeBrain_OASIS-TRT-20_labels.txt: preprocessing code for volumes* code_[re]postprocess_Mindboggle101_data.txt: postprocessing code code_resample2mm.txt: resampling code label_definitions.txt: labeling protocol (see above article) labels_on_fsaverage_surfaces.png: example labels subject_list_Mindboggle101.txt: list of subjects subject_scans_info_Mindboggle101.tar.gz: information about the scans subject_sources_Mindboggle101.txt: scan sources subject_table_Mindboggle101.pdf: table of subjects ShapeTables_mindboggle_20141017.tar.gz: features and shapes output by Mindboggle software

Biomarker assisted preclinical/early detection and intervention in Alzheimer’s disease (AD) may be the key to therapeutic breakthroughs. One of the presymptomatic hallmarks of AD is the accumulation of beta-amyloid (Aβ) plaques in the human brain. However, current methods to detect Aβ pathology are either invasive (lumbar puncture) or quite costly and not widely available (amyloid PET). Our prior studies show that magnetic resonance imaging (MRI)-based hippocampal multivariate morphometry statistics (MMS) are an effective neurodegenerative biomarker for preclinical AD. Here we attempt to use MRI-MMS to make inferences regarding brain Aβ burden at the individual subject level. As MMS data has a larger dimension than the sample size, we propose a sparse coding algorithm, Patch Analysis-based Surface Correntropy-induced Sparse-coding and Max-Pooling (PASCS-MP), to generate a low-dimensional representation of hippocampal morphometry for each individual subject. Then we apply these individual representations and a binary random forest classifier to predict brain Aβ positivity for each person. We test our method in two independent cohorts, 841 subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and 260 subjects from the Open Access Series of Imaging Studies (OASIS). Experimental results suggest that our proposed PASCS-MP method and MMS can discriminate Aβ positivity in people with mild cognitive impairment (MCI) [Accuracy (ACC) = 0.89 (ADNI)] and in cognitively unimpaired (CU) individuals [ACC = 0.79 (ADNI) and ACC = 0.81 (OASIS)]. These results compare favorably relative to measures derived from traditional algorithms, including hippocampal volume and surface area, shape measures based on spherical harmonics (SPHARM) and our prior Patch Analysis-based Surface Sparse-coding and Max-Pooling (PASS-MP) methods.

These files include a subset of the data used in the manuscript entitled 'Inserting an index of motion degradation into the analysis of MRI data (QUIQI)', and its associated set of analysis results. The code used to compile these results is available here: QUIQI Analysis script - inserting an index of motion degradation into the analysis of MRI data | Zenodo).

CONTENT

The provided data contains 123 datasets selected from the original cohort by sampling randomly up to 10 datasets in age bins of 5 years, ranging from 10 to 100 y.o.. These datasets are contained in separate folders labelled ‘sub-001’ to ‘sub-123’. Each dataset contains the following items:

- Contrast-specific R2* maps, computed from MT-, PD- and T1-weighted raw data. The corresponding data file names end with ‘_MTw_R2s’, ‘_PDw_R2s’, ‘_T1w_R2s’ respectively. Separate files are provided for voxels belonging to the grey and white matter tissue classes (files name with ‘p1’ and ‘p2’ respectively)

- Grey and white matter tissue probability maps (starting with ‘mwc1’ and ‘mwc2’ respectively), used for the computation of explicit masks for data analysis.

The provided data also contains the following items:

- Neuromorphometrics folder: grey matter atlas computed from the maximum probability tissue labels derived from the “MICCAI 2012 Grand Challenge and Workshop on Multi-Atlas Labeling” (https://masi.vuse.vanderbilt.edu/workshop2012/index.php/Challenge_Details), computed from MRI scans originating from the OASIS project (http://www.oasis-brains.org/) and labelled data provided by Neuromorphometrics, Inc. (http://neuromorphometrics.com/) under academic subscription.

- The folders Analysis_Full, Analysis_Residuals, Analysis_Exclusion and Analysis_Specificity contain the analysis results described in the original scientific publication, and obtained using the publicly available analysis code available here: .

- Subject_Details.mat: matlab structure containing the data information required for analysis.

BackgroundAccording to the World Health Organization (WHO), dementia is the seventh leading reason of death among all illnesses and one of the leading causes of disability among the world’s elderly people. Day by day the number of Alzheimer’s patients is rising. Considering the increasing rate and the dangers, Alzheimer’s disease should be diagnosed carefully. Machine learning is a potential technique for Alzheimer’s diagnosis but general users do not trust machine learning models due to the black-box nature. Even, some of those models do not provide the best performance because of using only neuroimaging data.ObjectiveTo solve these issues, this paper proposes a novel explainable Alzheimer’s disease prediction model using a multimodal dataset. This approach performs a data-level fusion using clinical data, MRI segmentation data, and psychological data. However, currently, there is very little understanding of multimodal five-class classification of Alzheimer’s disease.MethodFor predicting five class classifications, 9 most popular Machine Learning models are used. These models are Random Forest (RF), Logistic Regression (LR), Decision Tree (DT), Multi-Layer Perceptron (MLP), K-Nearest Neighbor (KNN), Gradient Boosting (GB), Adaptive Boosting (AdaB), Support Vector Machine (SVM), and Naive Bayes (NB). Among these models RF has scored the highest value. Besides for explainability, SHapley Additive exPlanation (SHAP) is used in this research work.Results and conclusionsThe performance evaluation demonstrates that the RF classifier has a 10-fold cross-validation accuracy of 98.81% for predicting Alzheimer’s disease, cognitively normal, non-Alzheimer’s dementia, uncertain dementia, and others. In addition, the study utilized Explainable Artificial Intelligence based on the SHAP model and analyzed the causes of prediction. To the best of our knowledge, we are the first to present this multimodal (Clinical, Psychological, and MRI segmentation data) five-class classification of Alzheimer’s disease using Open Access Series of Imaging Studies (OASIS-3) dataset. Besides, a novel Alzheimer’s patient management architecture is also proposed in this work.

BackgroundAccording to the World Health Organization (WHO), dementia is the seventh leading reason of death among all illnesses and one of the leading causes of disability among the world’s elderly people. Day by day the number of Alzheimer’s patients is rising. Considering the increasing rate and the dangers, Alzheimer’s disease should be diagnosed carefully. Machine learning is a potential technique for Alzheimer’s diagnosis but general users do not trust machine learning models due to the black-box nature. Even, some of those models do not provide the best performance because of using only neuroimaging data.ObjectiveTo solve these issues, this paper proposes a novel explainable Alzheimer’s disease prediction model using a multimodal dataset. This approach performs a data-level fusion using clinical data, MRI segmentation data, and psychological data. However, currently, there is very little understanding of multimodal five-class classification of Alzheimer’s disease.MethodFor predicting five class classifications, 9 most popular Machine Learning models are used. These models are Random Forest (RF), Logistic Regression (LR), Decision Tree (DT), Multi-Layer Perceptron (MLP), K-Nearest Neighbor (KNN), Gradient Boosting (GB), Adaptive Boosting (AdaB), Support Vector Machine (SVM), and Naive Bayes (NB). Among these models RF has scored the highest value. Besides for explainability, SHapley Additive exPlanation (SHAP) is used in this research work.Results and conclusionsThe performance evaluation demonstrates that the RF classifier has a 10-fold cross-validation accuracy of 98.81% for predicting Alzheimer’s disease, cognitively normal, non-Alzheimer’s dementia, uncertain dementia, and others. In addition, the study utilized Explainable Artificial Intelligence based on the SHAP model and analyzed the causes of prediction. To the best of our knowledge, we are the first to present this multimodal (Clinical, Psychological, and MRI segmentation data) five-class classification of Alzheimer’s disease using Open Access Series of Imaging Studies (OASIS-3) dataset. Besides, a novel Alzheimer’s patient management architecture is also proposed in this work.