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  • Neuroinformatics
  • 2014-2023
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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: Ioanas, Horea-Ioan; Marks, Markus; Segessemann, Tina; Schmidt, Dominik; +2 Authors

    SAMRI (Small Animal Magnetic Resonance Imaging) - pronounced "Sam-rye" - provides fMRI preprocessing, metadata parsing, and data analysis functions and pipelines. SAMRI integrates functionalities from a number of other packages (listed under the dependencies section below) to create higher-level tools. The resulting interfaces aim to maximize reproducibility, simplify batch processing, and minimize the number of function calls required to generate figures and statistical summaries from the raw data. The package is compatible with small rodent data acquired via Bruker systems.

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    ZENODO
    Software . 2019
    License: CC BY
    Data sources: ZENODO
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    ZENODO
    Software . 2019
    License: CC BY
    Data sources: ZENODO
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    ZENODO
    Software . 2019
    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/
    ZENODO
    Software . 2019
    License: CC BY
    Data sources: Datacite
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      ZENODO
      Software . 2019
      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/
      ZENODO
      Software . 2019
      License: CC BY
      Data sources: ZENODO
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      ZENODO
      Software . 2019
      License: CC BY
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      ZENODO
      Software . 2019
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      Data sources: Datacite
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    Authors: Lagorce, David; Villoutreix, Bruno;

    Process compound collections via simple absorption, distribution, metabolism, excretion and toxicity (ADME/tox) filtering rules to aid in the drug discovery process.

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    bio.tools
    Software . 2017
    License: Freeware
    Data sources: bio.tools
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      bio.tools
      Software . 2017
      License: Freeware
      Data sources: bio.tools
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    Authors: Tourbier, Sebastien; Aleman-Gomez, Yasser; Griffa, Alessandra; Bach Cuadra, Meritxell; +1 Authors

    This is the beta release v3.0.0-beta-20191021 of the Connectome Mapper. List of changes with respect to previous 3.0.0-beta-20190815: ENH: added color codes for colored printouts ENH: control/set the number of participants being processed in parallel ENH: update mrtrix 5ttgen FIX: high-pass filtering of BOLD FIX: Freesurfer license FIX: commented multiproc_number_of_cores FIX: remove hsperfdata_ folder generated in tmp/ at the end of BIDS App execution FIX: duplicate connection in fmri pipeline FIX: correct indent level for fmri pipeline FIX: extra self. removed for manage_processes() MAINT: added and commented git log command to generate changes between release MAINT: update version to -beta-20191021 DOC: updated readme with badges DOC: added zenodo doi badge DOC: updated Zenodo citation ZENODO: updated list of contributors

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    ZENODO
    Software . 2019
    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 . 2020
    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 . 2020
    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
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      ZENODO
      Software . 2019
      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 . 2020
      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 . 2020
      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: The tedana Community; Ahmed, Zaki; Bandettini, Peter A.; Bottenhorn, Katherine L.; +19 Authors

    Release Notes We have made this release candidate to test recent enhancements. Please open issues if you experience any problems. Changes [DOC] Add link to EuskalIBUR dataset in documentation (#780) @tsalo [FIX] Add resources folder to package data (#772) @tsalo [ENH] Use different masking thresholds for denoising and classification (#736) @tsalo [DOC, MAINT] Updated dependency version numbers (#763) @handwerkerd [REF] Move logger management to new functions (#750) @tsalo [FIX] Ignore non-significant kappa elbow when no non-significant kappa values exist (#760) @tsalo [ENH] Coerce images to 32-bit (#759) @jbteves [ENH] Add carpet plot to outputs (#696) @tsalo [FIX] Correct manacc documentation and check for associated inputs (#754) @tsalo [DOC] Reorganize documentation (#740) @tsalo [REF] Do not modify mixing matrix with sign-flipping (#749) @tsalo [REF] Eliminate component sorting from metric calculation (#741) @tsalo [FIX] Update apt in CircleCI (#746) @notZaki [DOC] Update resource page with dataset and link to Dash app visualizations (#745) @jsheunis [DOC] Clarify communication pathways (#742) @tsalo [FIX] Disable report logging during ICA restart loop (#743) @tsalo [REF] Replace metric dependency dictionaries with json file (#739) @tsalo [FIX] Add references back into the HTML report (#737) @tsalo [ENH] Allows iterative clustering (#732) @jbteves [REF] Modularize metric calculation (#591) @tsalo Rename sphinx functions to fix building error for docs (#727) @eurunuela [ENH] Generate BIDS Derivatives-compatible outputs (#691) @tsalo

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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: James Kent; Yarkoni, Tal; De La Vega, Alejandro; Lee, Nicholas;

    Release Notes Minor release, incorporate major bug fixes and recommendations from OHBM meeting. CHANGES [FIX] unique already creates an index, unique made a repetitive index (#600) @jdkent [ENH] add base_study attribute (#599) @jdkent [FIX] ignore string if doi/pmid/name string is empty (#598) @jdkent [ENH] add conditions and weights to specification (#597) @jdkent [ENH] add studyset-references endpoint (#596) @jdkent chore(deps): bump @cypress/request and cypress in /compose/neurosynth-frontend (#595) @dependabot 197 display user icon name (#591) @nicoalee [ENH] add username and neurostore studyset script (#590) @jdkent [FIX] nick feedback (#589) @jdkent [ENH] add usernames to compose (#588) @jdkent [MAINT] update openapi to main branch (#586) @jdkent [ENH] bulk upload (#585) @jdkent 565 update the advanced search input (#583) @nicoalee [ENH] add username as resource attribute (#584) @jdkent 561 switch api from studies to abstract studies (#582) @nicoalee [FIX] id not showing up for info=true (#581) @jdkent [ENH] using an iterator over a list comprehension should be faster (#578) @jdkent [FIX] add data_type to base_study (#577) @jdkent [FIX] info query param behavior (#576) @jdkent [ENH] make it quicker to filter studies by whether they have images/points. (#574) @jdkent chore(deps): bump tough-cookie and @cypress/request in /compose/neurosynth-frontend (#569) @dependabot

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    ZENODO
    Software . 2023
    Data sources: Datacite
    ZENODO
    Software . 2023
    Data sources: ZENODO
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      ZENODO
      Software . 2023
      Data sources: Datacite
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      Software . 2023
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  • Authors: Perović, Nemanja Stefan; Le-Nam Tran; Di Renzo, Marco; Flanagan, Mark F.;

    Simulation codes for "Optimization of RIS-aided MIMO Systems via the Cutoff Rate," by Nemanja Stefan Perović, Le-Nam Tran, Marco Di Renzo, and Mark F. Flanagan, IEEE Wireless Commun. Lett. , vol. 10, no.8, pp. 1692-1696, Aug. 2021.

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    Authors: Mühlau, Mark;

    Lesion Segmentation Tool (LST) is an open source toolbox for SPM that is able to segment T2 hyperintense lesions in FLAIR images. Originally developed for the segmentation of MS lesions it has has also been proven to be useful for the segmentation of brain lesions in the context of other diseases, such as diabetes mellitus or Alzheimers disease.

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    bio.tools
    Software . 2019
    License: GPL-3.0
    Data sources: bio.tools
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      bio.tools
      Software . 2019
      License: GPL-3.0
      Data sources: bio.tools
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    Authors: Dvorak, Adam V.;

    Example code for the multivariate template creation process used for Myelin imaging in the central nervous system: Comparison of multi-echo T2 relaxation and steady-state approaches

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    Authors: Flávio Luiz Cardoso-Ribeiro; Andrea Brugnoli; Denis Matignon; Laurent Lefèvre;

    This archive presents the source codes and numerical results of our paper "Port-Hamiltonian modeling, discretization and feedback control of a circular water tank", presented at the 2019 IEEE 58th Conference on Decision and Control (CDC), in Lyon, France. The paper is available here. https://github.com/flavioluiz/Circular-Tank-PFEM-CDC-supplementary-material The following codes are provided: codes/Saint_Venant1D.py: reduced model of the circular tank, considering radial symmetry (Figures 1 and 2 of the paper) codes/Saint_Venant2D.py: nonlinear 2D model with feedback control (Figures 3 and 4 of the paper) codes/AnimateSurf.py: auxiliary file used to obtain the animation. A GitHub with the codes is available here. How to install and run the code? The numerical FEM model is obtained thanks to FEniCS. Firstly, you need to install it. We suggest installing it from Anaconda, as described here (check the part FEniCS on Anaconda). Once installed, you need to activate the FEniCs environment: your@user:~$ conda activate fenicsproject Then, you just need to run the Python script on the environment: (fenicsproject) your@user:~$ python Saint_Venant2D.py The scripts were tested using Python 3.7, and FEniCS 2018.1.0. Acknowledgements This work has been performed in the frame of the Collaborative Research DFG and ANR project INFIDHEM, entitled "Interconnected of Infinite-Dimensional systems for Heterogeneous Media", nº ANR-16-CE92-0028. Further information is available here.

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    ZENODO
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    Authors: Cattan, Sarah; Molotchnikoff, Stéphane;

    Matlab scripts from a published paper in EJN : Comparative analysis of orientation maps in areas 17 and 18 of the cat primary visual cortex following adaptation. Cattan S1, Bachatene L, Bharmauria V, Jeyabalaratnam J, Milleret C, Molotchnikoff S. genererFiguresOri : main script to generate polar maps, orientation maps and number of pixels per presented orientation in A17 and A18. genererFIgures.m : second main file. Perform several computations on A17 and A18 maps. Figures computed by the script are not all in the paper. Several files ares dependences of these two main files. We recommend to first save all the files. Files c*.m : commands ran for each cat (cats number 5, 6, 7. 8, 9 and 10).

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    Authors: Ioanas, Horea-Ioan; Marks, Markus; Segessemann, Tina; Schmidt, Dominik; +2 Authors

    SAMRI (Small Animal Magnetic Resonance Imaging) - pronounced "Sam-rye" - provides fMRI preprocessing, metadata parsing, and data analysis functions and pipelines. SAMRI integrates functionalities from a number of other packages (listed under the dependencies section below) to create higher-level tools. The resulting interfaces aim to maximize reproducibility, simplify batch processing, and minimize the number of function calls required to generate figures and statistical summaries from the raw data. The package is compatible with small rodent data acquired via Bruker systems.

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    ZENODO
    Software . 2019
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    Authors: Lagorce, David; Villoutreix, Bruno;

    Process compound collections via simple absorption, distribution, metabolism, excretion and toxicity (ADME/tox) filtering rules to aid in the drug discovery process.

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    bio.tools
    Software . 2017
    License: Freeware
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      bio.tools
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    Authors: Tourbier, Sebastien; Aleman-Gomez, Yasser; Griffa, Alessandra; Bach Cuadra, Meritxell; +1 Authors

    This is the beta release v3.0.0-beta-20191021 of the Connectome Mapper. List of changes with respect to previous 3.0.0-beta-20190815: ENH: added color codes for colored printouts ENH: control/set the number of participants being processed in parallel ENH: update mrtrix 5ttgen FIX: high-pass filtering of BOLD FIX: Freesurfer license FIX: commented multiproc_number_of_cores FIX: remove hsperfdata_ folder generated in tmp/ at the end of BIDS App execution FIX: duplicate connection in fmri pipeline FIX: correct indent level for fmri pipeline FIX: extra self. removed for manage_processes() MAINT: added and commented git log command to generate changes between release MAINT: update version to -beta-20191021 DOC: updated readme with badges DOC: added zenodo doi badge DOC: updated Zenodo citation ZENODO: updated list of contributors

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    Authors: The tedana Community; Ahmed, Zaki; Bandettini, Peter A.; Bottenhorn, Katherine L.; +19 Authors

    Release Notes We have made this release candidate to test recent enhancements. Please open issues if you experience any problems. Changes [DOC] Add link to EuskalIBUR dataset in documentation (#780) @tsalo [FIX] Add resources folder to package data (#772) @tsalo [ENH] Use different masking thresholds for denoising and classification (#736) @tsalo [DOC, MAINT] Updated dependency version numbers (#763) @handwerkerd [REF] Move logger management to new functions (#750) @tsalo [FIX] Ignore non-significant kappa elbow when no non-significant kappa values exist (#760) @tsalo [ENH] Coerce images to 32-bit (#759) @jbteves [ENH] Add carpet plot to outputs (#696) @tsalo [FIX] Correct manacc documentation and check for associated inputs (#754) @tsalo [DOC] Reorganize documentation (#740) @tsalo [REF] Do not modify mixing matrix with sign-flipping (#749) @tsalo [REF] Eliminate component sorting from metric calculation (#741) @tsalo [FIX] Update apt in CircleCI (#746) @notZaki [DOC] Update resource page with dataset and link to Dash app visualizations (#745) @jsheunis [DOC] Clarify communication pathways (#742) @tsalo [FIX] Disable report logging during ICA restart loop (#743) @tsalo [REF] Replace metric dependency dictionaries with json file (#739) @tsalo [FIX] Add references back into the HTML report (#737) @tsalo [ENH] Allows iterative clustering (#732) @jbteves [REF] Modularize metric calculation (#591) @tsalo Rename sphinx functions to fix building error for docs (#727) @eurunuela [ENH] Generate BIDS Derivatives-compatible outputs (#691) @tsalo

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    Authors: James Kent; Yarkoni, Tal; De La Vega, Alejandro; Lee, Nicholas;

    Release Notes Minor release, incorporate major bug fixes and recommendations from OHBM meeting. CHANGES [FIX] unique already creates an index, unique made a repetitive index (#600) @jdkent [ENH] add base_study attribute (#599) @jdkent [FIX] ignore string if doi/pmid/name string is empty (#598) @jdkent [ENH] add conditions and weights to specification (#597) @jdkent [ENH] add studyset-references endpoint (#596) @jdkent chore(deps): bump @cypress/request and cypress in /compose/neurosynth-frontend (#595) @dependabot 197 display user icon name (#591) @nicoalee [ENH] add username and neurostore studyset script (#590) @jdkent [FIX] nick feedback (#589) @jdkent [ENH] add usernames to compose (#588) @jdkent [MAINT] update openapi to main branch (#586) @jdkent [ENH] bulk upload (#585) @jdkent 565 update the advanced search input (#583) @nicoalee [ENH] add username as resource attribute (#584) @jdkent 561 switch api from studies to abstract studies (#582) @nicoalee [FIX] id not showing up for info=true (#581) @jdkent [ENH] using an iterator over a list comprehension should be faster (#578) @jdkent [FIX] add data_type to base_study (#577) @jdkent [FIX] info query param behavior (#576) @jdkent [ENH] make it quicker to filter studies by whether they have images/points. (#574) @jdkent chore(deps): bump tough-cookie and @cypress/request in /compose/neurosynth-frontend (#569) @dependabot

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