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67 Research products

  • Neuroinformatics
  • 2023-2023
  • 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: 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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  • 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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  • 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; 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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  • 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: Muhammad Fahad; Kim Sontheimer; Rolando Ingles; Wouter Klijn; +4 Authors

    The v2.0 official release of the Modular Science Framework for multi-scale Co-simulations. The main focus of this release is to improve the framework's usability and broaden its functionality, with a focus on integrating additional neuroscience use-cases. These include: Real-time calculation of Local Field Potentials (LFPs) based on spike events streamed from the NEST simulation. Integration of NEST Desktop, Insite pipeline, and Modular Science - Multiscale Co-simulation. Significant modifications have been implemented in the core modules, particularly RichEndpoint and Interscale Hub, with the aim of enhancing their efficiency, extensibility, and modularity to seamlessly accommodate forthcoming use-cases. The release notes for this release are available at Modular Science Framework v2.0.

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    Authors: Masoud, Mohamed; Hu, Farfalla; Plis, Sergey;

    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 Doc: Github Wiki For local setup please follow these instructions In v2.1.0, brainchop code and paper revised as per Journal of Open Source Software (JOSS) reviewers requested. Brainchop was funded by the NIH grant RF1MH121885. Additional support from NIH R01MH123610, R01EB006841 and NSF 2112455.

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    Authors: Dustin Moraczewski;

    This repo provides shell scripts to help summarize fmriprep error reports across an entire dataset and to generate motion censor files from the fmriprep confounds.

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    Authors: Domenic H Cerri;

    Accompanying manuscript preprint can be found here: https://www.biorxiv.org/content/10.1101/2023.02.20.529283v1 Subfolders indicate data type(s) Data processing, analysis, and visualization scripts and pipelines, along with respective instructions and dependencies can be found within each subfolder.

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    Authors: Christian Paret;

    This code version was released before submission of the original manuscript to a peer-reviewed journal. Before using this code it is recommended to check whether there is a more recent releas

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    Authors: Tisca, Cristiana; Tachrount, Mohamed; Lange, Frederik J; Wang, Chaoyue; +4 Authors

    {"references": ["Bautista, T. et al. (2021) 'Removal of Gibbs ringing artefacts for 3D acquisitions using subvoxel shifts', in Proc. Intl. Soc. Mag. Reson. Med., p. 3535.", "Chakravarty, M. M. et al. (2013) 'Performing label-fusion-based segmentation using multiple automatically generated templates', Human Brain Mapping. doi: 10.1002/hbm.22092.", "Eckstein, K. et al. (2018) 'Computationally Efficient Combination of Multi-channel Phase Data From Multi-echo Acquisitions (ASPIRE)', Magnetic Resonance in Medicine, 79(6), pp. 2996\u20133006. doi: 10.1002/mrm.26963.", "Friedel, M. et al. (2014) 'Pydpiper: A flexible toolkit for constructing novel registration pipelines', Frontiers in Neuroinformatics. doi: 10.3389/fninf.2014.00067.", "Gudbjartsson, H. and Patz, S. (1995) 'The rician distribution of noisy MRI data', Magnetic Resonance in Medicine, 34(6), pp. 910\u2013914. doi: 10.1002/mrm.1910340618.", "Jenkinson, M. (2003) 'Fast, automated, N-dimensional phase-unwrapping algorithm', Magnetic Resonance in Medicine, 49(1), pp. 193\u2013197. doi: 10.1002/mrm.10354.", "Kellner, E. et al. (2016) 'Gibbs-ringing artifact removal based on local subvoxel-shifts', Magnetic Resonance in Medicine. doi: 10.1002/mrm.26054.", "Li, W. et al. (2015) 'A method for estimating and removing streaking artifacts in quantitative susceptibility mapping', NeuroImage. doi: 10.1016/j.neuroimage.2014.12.043.", "Li, W., Wu, B. and Liu, C. (2011) 'Quantitative susceptibility mapping of human brain reflects spatial variation in tissue composition', NeuroImage. doi: 10.1016/j.neuroimage.2010.11.088.", "Robinson, S. D. et al. (2017) 'Combining phase images from array coils using a short echo time reference scan (COMPOSER)', Magnetic Resonance in Medicine. doi: 10.1002/mrm.26093.", "Schweser, F. et al. (2011) 'Quantitative imaging of intrinsic magnetic tissue properties using MRI signal phase: An approach to in vivo brain iron metabolism?', NeuroImage. doi: 10.1016/j.neuroimage.2010.10.070.", "Tisca, C. et al. (2021) 'Vcan mutation induces sex-specific changes in white matter microstructure in mice', in Proc. Intl. Soc. Mag. Reson. Med. 29, p. 1226. Available at: https://index.mirasmart.com/ISMRM2021/PDFfiles/1226.html.", "Tisca, C. et al. (2022) 'White matter microstructure changes in a Bcan knockout mouse model', in Proc. Intl. Soc. Mag. Reson. Med. 31.", "Wang, C. et al. (2020) 'Methods for quantitative susceptibility and R2* mapping in whole post-mortem brains at 7T applied to amyotrophic lateral sclerosis', NeuroImage. Elsevier Inc., 222(May), p. 117216. doi: 10.1016/j.neuroimage.2020.117216.", "Wang, C. et al. (2022) 'Phenotypic and genetic associations of quantitative magnetic susceptibility in UK Biobank brain imaging', Nature Neuroscience, 25(6), pp. 818\u2013831. doi: 10.1038/s41593-022-01074-w."]} This repository contains all scripts to run the ex vivo R2*- and QSM post-processing pipelines on data acquired at WIN's 7T Bruker facility. It should be compatible with any other data acquired on a similar Bruker scanner using an equivalent protocol. This resource contains anonymised file-paths which will need to be edited to enable running on a cluster facility. The commands for submitting jobs to the cluster also need to be edited. This pipeline is based on the code developed by Chaoyue Wang and Benjamin Tendler and published here: https://doi.org/10.1016/j.neuroimage.2020.117216. The scripts were either written or adapted by Cristiana Tisca. The outputs of the pipeline include QSM and R2* maps. Additional funding sources: Wellcome Trust Senior Research Fellowship (Renewal), Prof Karla Miller, 224573/Z/21/Z

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    Authors: Pramod Kumar Pisharady,;

    ALS Multimodal Analysis Source Code This software package provides the MATLAB codes and shell scripts used to produce the results reported in the paper ‘Improved Diagnostic Accuracy and Sensitivity to Longitudinal Change in ALS with Multimodal MRI of the Brain and Cervical Cord’. Citation: Pisharady PK, Eberly LE et al. Improved Diagnostic Accuracy and Sensitivity to Longitudinal Change in ALS with Multimodal MRI of the Brain and Cervical Cord, 30 September 2022, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-2091268/v1]

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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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  • 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: 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: Muhammad Fahad; Kim Sontheimer; Rolando Ingles; Wouter Klijn; +4 Authors

    The v2.0 official release of the Modular Science Framework for multi-scale Co-simulations. The main focus of this release is to improve the framework's usability and broaden its functionality, with a focus on integrating additional neuroscience use-cases. These include: Real-time calculation of Local Field Potentials (LFPs) based on spike events streamed from the NEST simulation. Integration of NEST Desktop, Insite pipeline, and Modular Science - Multiscale Co-simulation. Significant modifications have been implemented in the core modules, particularly RichEndpoint and Interscale Hub, with the aim of enhancing their efficiency, extensibility, and modularity to seamlessly accommodate forthcoming use-cases. The release notes for this release are available at Modular Science Framework v2.0.

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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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      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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      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
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      Data sources: Datacite