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311 Research products

  • Neuroinformatics
  • 2019-2023
  • Open Access
  • Research software

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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.

    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
    Software . 2019
    License: CC BY
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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/
    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
    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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      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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      Software . 2019
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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/
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      Software . 2019
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      Software . 2019
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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/
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      Software . 2019
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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: 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
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    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/
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    Software . 2020
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      ZENODO
      Software . 2019
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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/
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      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/
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      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: 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
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    Software . 2023
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      Software . 2023
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      Software . 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: 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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    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/
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    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/ ZENODOarrow_drop_down
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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/
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      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: 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
    Software . 2020
    Data sources: Datacite
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    Software . 2020
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    Authors: Kaczmarzyk, Jakub; McClure, Patrick; Zulfikar, Wazeer; Rana, Aakanksha; +6 Authors

    🚀 Enhancement Update README.md and move transforms #187 (@Hoda1394 @pre-commit-ci[bot] @satra) 🐛 Bug Fix Documentation update #184 (@Aakanksha-Rana @pre-commit-ci[bot] @satra) Correction of G_dice and multi_class dice_calculation #164 (@kaczmarj @Aakanksha-Rana @pre-commit-ci[bot] @satra) DOC: Update link to CITATION file #190 (@arokem) Bayesian: 3D bayes_by_backprop_layer + Distributed Weight Consolidation #185 (@Aakanksha-Rana @pre-commit-ci[bot] @satra) [pre-commit.ci] pre-commit autoupdate #188 (@pre-commit-ci[bot]) Fix tf & tfp compatibility with python version #186 (@Hoda1394 @satra) [pre-commit.ci] pre-commit autoupdate #183 (@pre-commit-ci[bot]) Added Clipping constraint and KLD loss with CD #180 (@Aakanksha-Rana @pre-commit-ci[bot] @satra) ENH: Allow multichannel input #177 (@richford @satra) Add citation #181 (@Aakanksha-Rana @pre-commit-ci[bot] @satra) [pre-commit.ci] pre-commit autoupdate #182 (@pre-commit-ci[bot]) adding brain siamese network models and test cases #172 (@dhritimandas @pre-commit-ci[bot] @satra) Added dcgan architecture with tests #66 (@wazeerzulfikar @pre-commit-ci[bot] @satra) BF: Add block_length param to dataset.interleave #175 (@richford @satra) Weightnorm feature for Variational layer #166 (@Aakanksha-Rana @pre-commit-ci[bot] @satra) [pre-commit.ci] pre-commit autoupdate #179 (@pre-commit-ci[bot]) [pre-commit.ci] pre-commit autoupdate #178 (@pre-commit-ci[bot]) [pre-commit.ci] pre-commit autoupdate #173 (@pre-commit-ci[bot]) [pre-commit.ci] pre-commit autoupdate #170 (@pre-commit-ci[bot]) [pre-commit.ci] pre-commit autoupdate #165 (@pre-commit-ci[bot]) [pre-commit.ci] pre-commit autoupdate #163 (@pre-commit-ci[bot]) fix: readme to remove qualified install #162 (@satra @pre-commit-ci[bot]) fix: remove unnecessary step in release action #158 (@satra) ⚠️ Pushed to master Update .zenodo.json (@satra) Authors: 9 @pre-commit-ci[bot] Aakanksha Rana (@Aakanksha-Rana) Adam Richie-Halford (@richford) Ariel Rokem (@arokem) Dhritiman Das (@dhritimandas) Hoda Rajaei (@Hoda1394) Jakub Kaczmarzyk (@kaczmarj) Satrajit Ghosh (@satra) Wazeer Zulfikar (@wazeerzulfikar)

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    XCP-D paves the final section of the reproducible and scalable route from the MRI scanner to functional connectivity data in the hands of neuroscientists. We developed XCP-D to extend the BIDS and NiPrep apparatus to the point where data is most commonly consumed and analyzed by neuroscientists studying functional connectivity. Thus, with the development of XCP-D, data can be automatically preprocessed and analyzed in BIDS format, using NiPrep-style containerized code, all the way from the from the scanner to functional connectivity matrices. If you use this software, please cite it using the metadata from this file.

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    Authors: Gau, Rémi; Barilari, Marco; Battal, Ceren; Rezk, Mohamed; +13 Authors

    bidspm is a set of pipelines and tools for Octave / MATLAB to process and analyze BIDS data sets using SPM12. Please check the code at: https://github.com/cpp-lln-lab/bidspm

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    Authors: Mohamed Masoud, Farfalla Hu and Sergey Plis;

    Brainchop is a client-side web-application for automatic segmentation of MRI volumes that brings automatic volumetric segmentation capability to neuroimaging by running a robustly pre-trained deep learning model. The app does not require technical sophistication from the user and is designed for locally and privately segmenting user’s T1 volumes. Results of the segmentation may be easily saved locally after the computation. An intuitive interactive interface that does not require any special training nor specific instruction to run enables access to a state of the art deep learning brain segmentation for anyone with a modern browser (e.g. Firefox, Chrome etc) and commonly available hardware. Additionally, we make implementation of brainchop freely available releasing its pure Javascript code as open-source. Online Demo: brainchop.org Source: Github Repo For local setup please follow these instructions

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    Authors: Larroque, Stephen Karl; Carrière, Manon; Martial, Charlotte; Laureys, Steven;

    A clinical and research 3T MRI protocol under 30 minutes. Includes sub-second BOLD functional MRI, multi-shell DWI/DTI, high-resolution structural MPRAGE-like MRI called FLAWS with automatic segmentation of grey, white matters and CSF, SWI, FLAIR and PC-ASL-3D. There is no difference with v1.1.2 apart from DOI.

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    Software . 2021
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311 Research products
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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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    Software . 2019
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    Software . 2019
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    ZENODO
    Software . 2019
    License: CC BY
    Data sources: Datacite
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      Software . 2019
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      Software . 2019
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      Software . 2019
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      Software . 2019
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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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    Software . 2020
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    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: 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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    Software . 2023
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