The Anatomical Tracings of Lesions after Stroke (ATLAS) Dataset - Release 1.2, 2018 (ICPSR 36684)

Version Date: Nov 27, 2018

Principal Investigator(s):
Sook-Lei Liew, USC Chan Division of Occupational Science & Occupational Therapy, University of Southern California

https://doi.org/10.3886/ICPSR36684.v3

Version V3 ()

  • V5 [2022-08-08]
  • V4 [2021-12-01] unpublished
  • V3 [2018-11-27] unpublished
  • V2 [2017-12-22] unpublished
  • V1 [2017-08-25] unpublished

You are currently viewing an older version of this data collection. A more recent version may be available by selecting ()

Additional information about this collection can be found in Version History.

2018-11-27 This study was updated with corrections to images in Cohorts 1 and 2 in the previous dataset. The study also included a new version of the metadata data file. The ICPSR codebook has also been updated based on that file.

2018-02-15 The citation of this study may have changed due to the new version control system that has been implemented. The previous citation was:

  • Liew, Sook-Lei. The Anatomical Tracings of Lesions after Stroke (ATLAS) Dataset - Release 1.2, 2018. ICPSR36684-v3. Ann Arbor, MI: Inter-university Consortium for Political and Social Research [distributor], 2018-11-27. http://doi.org/10.3886/ICPSR36684.v3

2017-12-22 This study was updated in order to include a new version of the metadata data files and a supplementary information scanner header attributes document. The ICPSR codebook has therefore also been updated.

2017-08-24 ICPSR data undergo a confidentiality review and are altered when necessary to limit the risk of disclosure. ICPSR also routinely creates ready-to-go data files along with setups in the major statistical software formats as well as standard codebooks to accompany the data. In addition to these procedures, ICPSR performed the following processing steps for this data collection:

  • Created variable labels and/or value labels.
  • Performed recodes and/or calculated derived variables.

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Alternate Title

ATLAS

Summary

To access this data collection, please click on the Restricted Data button above. You will need to download and complete the data use agreement and then email it to icpsr-addep@umich.edu. The instructions are in the form.

The Anatomical Tracings of Lesions After Stroke (ATLAS) Dataset - Release 1.2 is an open-source data collection consisting a total of 304 T1-weighted MRIs (Magnetic Resonance Imaging) with manually segmented diverse lesions and metadata. The goal of ATLAS is to provide the research community with a standardized training and testing dataset for lesion segmentation algorithms on T1-weighted MRIs.

From 11 cohorts worldwide, 304 MRI images were collected from research groups in the ENIGMA Stroke Recovery Working Group consortium. Images consisted of T1-weighted anatomical MRIs of individuals after stroke. For each MRI, brain lesions were identified and masks were manually drawn on each individual brain in native space using MRIcron, an open-source tool for brain imaging visualization and defining volumes of interest. A minimum of one lesion mask was identified for each individual MRI. If additional, separate lesions were identified, they were traced as separate masks. A separate tracer performed quality control on each lesion mask. This included assessing the accuracy of the lesion segmentations, revising the lesion mask if needed, and categorizing the lesions to generate additional data such as lesion location. In addition, an expert neuroradiologist reviewed all lesions to provide additional qualitative descriptions of the type of stroke, vascular territory, and intensity of white matter disease. This dataset is provided in both native subject space and normalized to a standard template (the MNI-152 template).

Citation

Liew, Sook-Lei. The Anatomical Tracings of Lesions after Stroke (ATLAS) Dataset - Release 1.2, 2018. Inter-university Consortium for Political and Social Research [distributor], 2018-11-27. https://doi.org/10.3886/ICPSR36684.v3

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Funding

Center for Large Data Research and Data Sharing in Rehabilitation (P2CHD06570)

Subject Terms

Geographic Coverage

Smallest Geographic Unit

None

Restrictions

This data collection may not be used for any purpose other than statistical reporting and analysis. Use of these data to learn the identity of any person or establishment is prohibited. To obtain the restricted data, users must complete the Restricted Data Use Agreement available for download from the Dataset(s) section of this study home page. Users must agree to the terms and conditions of the agreement and send the form to ADDEP staff.

Distributor(s)

Inter-university Consortium for Political and Social Research
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Time Period(s)

2018

Data Collection Notes

  1. Before analyzing the data, users are encouraged to review the README file and the PI Documentation file, both available for download from the study home page. Please contact ADDEP staff at icpsr-addep@umich.edu for further information about the data.

    Users are also encouraged to refer to the bioRxiv article for any additional information about the study.

  2. Lesions were segmented using the NITRC open source software MRIcron which can be downloaded from the NITRC website. Users can also quickly and easily view the brains on BrainBox, an open-source Web application to collaboratively annotate and segment neuroimaging data available online. For additional quick quantification, a small toolbox was created. It is called SRQL (Semi-automated Robust Quantification of Lesions), which includes three features: it uses a semi-automated white matter intensity correction, outputs a report of descriptive statistics on lesions, and gives users the option to perform analyses in native or standard space. Finally, any issues or feedback can be submitted on the ATLAS GitHub page, on which any updates, software, and additional releases will also be announced.
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Study Design

Research groups in the ENIGMA Stroke Recovery Working Group consortium collected 304 MRI images from 11 cohorts worldwide. Images consisted of T1-weighted anatomical MRIs of individuals after stroke. For each MRI, brain lesions were identified and masks were manually drawn on each individual brain in native space using MRIcron, an open-source tool for brain imaging visualization and defining volumes of interest. A minimum of one lesion mask was identified for each individual MRI. If additional, separate lesions were identified, they were traced as separate masks. A separate tracer performed quality control on each lesion mask. This included assessing the accuracy of the lesion segmentations, revising the lesion mask if needed, and categorizing the lesions to generate additional data such as lesion location. In addition, an expert neuroradiologist reviewed all lesions to provide additional qualitative descriptions of the type of stroke, vascular territory, and intensity of white matter disease. The data collection is provided in both native subject space and normalized to a standard template (the MNI-152 template).

Sample

Convenience samples at 11 different locations worldwide.

Time Method

Cross-sectional

Universe

MRIs of individuals from around the world who have suffered a stroke.

Unit(s) of Observation

Individual

Data Type(s)

Mode of Data Collection

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Original Release Date

2017-08-24

Version History

2018-11-27 This study was updated with corrections to images in Cohorts 1 and 2 in the previous dataset. The study also included a new version of the metadata data file. The ICPSR codebook has also been updated based on that file.

2018-02-15 The citation of this study may have changed due to the new version control system that has been implemented. The previous citation was:
  • Liew, Sook-Lei. The Anatomical Tracings of Lesions after Stroke (ATLAS) Dataset - Release 1.2, 2018. ICPSR36684-v3. Ann Arbor, MI: Inter-university Consortium for Political and Social Research [distributor], 2018-11-27. http://doi.org/10.3886/ICPSR36684.v3

2017-12-22 This study was updated in order to include a new version of the metadata data files and a supplementary information scanner header attributes document. The ICPSR codebook has therefore also been updated.

2017-08-24 ICPSR data undergo a confidentiality review and are altered when necessary to limit the risk of disclosure. ICPSR also routinely creates ready-to-go data files along with setups in the major statistical software formats as well as standard codebooks to accompany the data. In addition to these procedures, ICPSR performed the following processing steps for this data collection:

  • Created variable labels and/or value labels.
  • Performed recodes and/or calculated derived variables.
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Weight

None

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