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  • Neuroinformatics
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Klein, Arno; Ghosh, Satrajit;

    Figure 2 - Examples of automatically extracted features (MRI) (a) Example structural features (left lateral views of volumes, surfaces, curves, and points) (b) Schematic feature hierarchy: 3-D gyrii surround a 2-D sulcal ribbon with 1-D fundus containing 0-D pits

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Image . 2016
    License: CC BY
    Data sources: ZENODO
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Image . 2016
      License: CC BY
      Data sources: ZENODO
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Klein, Arno; Ghosh, Satrajit;

    Figure 3 - Example of a graph-based representation of MRI and DTI features (a) A gray/white matter surface (left lateral view) with (visible) sulcal pits highlighted. These features go by different names (sulcal roots, buried gyrii, annectant gyrii, plis de passage) and may be well conserved structures formed early in development. (b) DTI connectivity graph computed on the same patient with depression as on the left panel. Vertices represent automatically extracted sulcal pits and each edge indicates a connection probability greater than 0.01 between two vertices.

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    ZENODO
    Image . 2016
    License: CC BY
    Data sources: ZENODO
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Image . 2016
      License: CC BY
      Data sources: ZENODO
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Klein, Arno; Ghosh, Satrajit;

    Figure 1 - Examples of graph-based representations of scientific data among hundreds on the www.visualcomplexity.com website (categories on the site include biology, food webs and semantic, social, and knowledge networks). Lower left images of DTI, connectome, and network hubs are from Olaf Sporns (2010, Scholarpedia, 5(2):5584).

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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    ZENODO
    Image . 2016
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      ZENODO
      Image . 2016
      License: CC BY
      Data sources: ZENODO
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Elliot A. Layden;

    NIfTI-Studio is a Matlab toolbox enabling researchers to visualize 3D NIfTI and Analyze images. Users can flip through slices, change orientations, 3D render surfaces, plot mosaics of slices, or add statistical overlays. NIfTI-Studio also allows for the manual creation of regions of interest (ROIs) to support additional analyses. The toolbox features an intuitive user interface that is easy to learn, but users also have the option to perform nearly all tasks via command line calls. The toolbox was designed for use with MRI brain imaging data, but it should be compatible with any NIfTI or Analyze format images.

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    ZENODO
    Software . 2020
    Data sources: ZENODO
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      ZENODO
      Software . 2020
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Avery, James; Goren, Nir; Mackle, Eleanor; Dowrick, Thomas; +2 Authors

    The UCLH Stroke EIT Dataset - Subject Data Each folder contains the raw data for each subject recording. Full details on the use of these files are given the repository https://github.com/EIT-team/Stroke_EIT_Dataset

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    ZENODO
    Dataset . 2017
    License: CC BY
    Data sources: ZENODO
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2017
      License: CC BY
      Data sources: ZENODO
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Klein, Arno;

    Figure 1 - Mindboggle schematic

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    ZENODO
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      ZENODO
      Image . 2016
      License: CC BY
      Data sources: ZENODO
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Gau, Rémi;

    Creates a neuroimaging cohort by aggregating data across datasets. If you use this software, please cite it as below.

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    ZENODO
    Software . 2023
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Software . 2023
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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      ZENODO
      Software . 2023
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Software . 2023
      Data sources: Datacite
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Klein, Arno;

    Figure 2 - Schematic of Mindboggle's graph-based database of anatomical features. Top: different structures derived from brain images: surface patches fragmented by application of the Laplace-Beltrami operator, sulcus folds and subfolds, and structures within a subfold. Bottom: schematic graph diagrams representing the relationships among the nested structures. Bottom right: examples of features as properties of edges (relationships such as Part of, Connected to, Has label) and nodes (geometric, shape, and spectral measures).

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    ZENODO
    Image . 2016
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      ZENODO
      Image . 2016
      License: CC BY
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    Authors: Klein, Arno;

    Figure 3 - Example of natural morphological variability: left inferior parietal lobule (IPL; figure from [Kiriyama et al. 2009]). (A-D) are MRI data and (E-G) are post-mortem specimens. (A) IPL is highlighted and folds are outlined. (B,E) Typical folding pattern. (C,F) PreSMG pattern: an additional gyrus (ellipse) lies between postCS and SMG. (D,G) PreAG pattern: an additional gyrus (ellipse) lies between SMG and AG. [SMG: supramarginal gyrus; AG: angular gyrus; postCS: postcentral sulcus; IPS: intraparietal sulcus; Sy: Sylvian fissure, STS: superior temporal sulcus; *sulcus intermedius primus] postCS IPS * * Sy STS IPL

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    ZENODO
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      ZENODO
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    Authors: Klein, Arno;

    Figure 5 - Mindboggle features and schematic diagram

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    Authors: Klein, Arno; Ghosh, Satrajit;

    Figure 2 - Examples of automatically extracted features (MRI) (a) Example structural features (left lateral views of volumes, surfaces, curves, and points) (b) Schematic feature hierarchy: 3-D gyrii surround a 2-D sulcal ribbon with 1-D fundus containing 0-D pits

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    Authors: Klein, Arno; Ghosh, Satrajit;

    Figure 3 - Example of a graph-based representation of MRI and DTI features (a) A gray/white matter surface (left lateral view) with (visible) sulcal pits highlighted. These features go by different names (sulcal roots, buried gyrii, annectant gyrii, plis de passage) and may be well conserved structures formed early in development. (b) DTI connectivity graph computed on the same patient with depression as on the left panel. Vertices represent automatically extracted sulcal pits and each edge indicates a connection probability greater than 0.01 between two vertices.

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    Authors: Klein, Arno; Ghosh, Satrajit;

    Figure 1 - Examples of graph-based representations of scientific data among hundreds on the www.visualcomplexity.com website (categories on the site include biology, food webs and semantic, social, and knowledge networks). Lower left images of DTI, connectome, and network hubs are from Olaf Sporns (2010, Scholarpedia, 5(2):5584).

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    Authors: Elliot A. Layden;

    NIfTI-Studio is a Matlab toolbox enabling researchers to visualize 3D NIfTI and Analyze images. Users can flip through slices, change orientations, 3D render surfaces, plot mosaics of slices, or add statistical overlays. NIfTI-Studio also allows for the manual creation of regions of interest (ROIs) to support additional analyses. The toolbox features an intuitive user interface that is easy to learn, but users also have the option to perform nearly all tasks via command line calls. The toolbox was designed for use with MRI brain imaging data, but it should be compatible with any NIfTI or Analyze format images.

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    Authors: Avery, James; Goren, Nir; Mackle, Eleanor; Dowrick, Thomas; +2 Authors

    The UCLH Stroke EIT Dataset - Subject Data Each folder contains the raw data for each subject recording. Full details on the use of these files are given the repository https://github.com/EIT-team/Stroke_EIT_Dataset

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    Dataset . 2017
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    Authors: Klein, Arno;

    Figure 1 - Mindboggle schematic

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    Authors: Gau, Rémi;

    Creates a neuroimaging cohort by aggregating data across datasets. If you use this software, please cite it as below.

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    Authors: Klein, Arno;

    Figure 2 - Schematic of Mindboggle's graph-based database of anatomical features. Top: different structures derived from brain images: surface patches fragmented by application of the Laplace-Beltrami operator, sulcus folds and subfolds, and structures within a subfold. Bottom: schematic graph diagrams representing the relationships among the nested structures. Bottom right: examples of features as properties of edges (relationships such as Part of, Connected to, Has label) and nodes (geometric, shape, and spectral measures).

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