LayNii: A software suite for layer-fMRI

•A new software toolbox is introduced for layer-specific functional MRI: LayNii.•LayNii is a suite of command-line executable C++ programs for Linux, Windows, and macOS.•LayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints.•LayNii performs layerification in the native...

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Vydané v:NeuroImage (Orlando, Fla.) Ročník 237; s. 118091
Hlavní autori: Huber, Laurentius (Renzo), Poser, Benedikt A., Bandettini, Peter A., Arora, Kabir, Wagstyl, Konrad, Cho, Shinho, Goense, Jozien, Nothnagel, Nils, Morgan, Andrew Tyler, van den Hurk, Job, Müller, Anna K, Reynolds, Richard C., Glen, Daniel R., Goebel, Rainer, Gulban, Omer Faruk
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States Elsevier Inc 15.08.2021
Elsevier Limited
Elsevier
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ISSN:1053-8119, 1095-9572, 1095-9572
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Abstract •A new software toolbox is introduced for layer-specific functional MRI: LayNii.•LayNii is a suite of command-line executable C++ programs for Linux, Windows, and macOS.•LayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints.•LayNii performs layerification in the native voxel space of functional data.•LayNii performs layer-smoothing, GE-BOLD deveining, QA, and VASO analysis. High-resolution fMRI in the sub-millimeter regime allows researchers to resolve brain activity across cortical layers and columns non-invasively. While these high-resolution data make it possible to address novel questions of directional information flow within and across brain circuits, the corresponding data analyses are challenged by MRI artifacts, including image blurring, image distortions, low SNR, and restricted coverage. These challenges often result in insufficient spatial accuracy of conventional analysis pipelines. Here we introduce a new software suite that is specifically designed for layer-specific functional MRI: LayNii. This toolbox is a collection of command-line executable programs written in C/C++ and is distributed opensource and as pre-compiled binaries for Linux, Windows, and macOS. LayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints and thus cannot be straightforwardly analyzed in alternative software packages. Some of the most popular programs of LayNii contain ‘layerification’ and columnarization in the native voxel space of functional data as well as many other layer-fMRI specific analysis tasks: layer-specific smoothing, model-based vein mitigation of GE-BOLD data, quality assessment of artifact dominated sub-millimeter fMRI, as well as analyses of VASO data. [Display omitted]
AbstractList High-resolution fMRI in the sub-millimeter regime allows researchers to resolve brain activity across cortical layers and columns non-invasively. While these high-resolution data make it possible to address novel questions of directional information flow within and across brain circuits, the corresponding data analyses are challenged by MRI artifacts, including image blurring, image distortions, low SNR, and restricted coverage. These challenges often result in insufficient spatial accuracy of conventional analysis pipelines. Here we introduce a new software suite that is specifically designed for layer-specific functional MRI: LayNii. This toolbox is a collection of command-line executable programs written in C/C++ and is distributed opensource and as pre-compiled binaries for Linux, Windows, and macOS. LayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints and thus cannot be straightforwardly analyzed in alternative software packages. Some of the most popular programs of LayNii contain ‘layerification’ and columnarization in the native voxel space of functional data as well as many other layer-fMRI specific analysis tasks: layer-specific smoothing, model-based vein mitigation of GE-BOLD data, quality assessment of artifact dominated sub-millimeter fMRI, as well as analyses of VASO data.
•A new software toolbox is introduced for layer-specific functional MRI: LayNii.•LayNii is a suite of command-line executable C++ programs for Linux, Windows, and macOS.•LayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints.•LayNii performs layerification in the native voxel space of functional data.•LayNii performs layer-smoothing, GE-BOLD deveining, QA, and VASO analysis. High-resolution fMRI in the sub-millimeter regime allows researchers to resolve brain activity across cortical layers and columns non-invasively. While these high-resolution data make it possible to address novel questions of directional information flow within and across brain circuits, the corresponding data analyses are challenged by MRI artifacts, including image blurring, image distortions, low SNR, and restricted coverage. These challenges often result in insufficient spatial accuracy of conventional analysis pipelines. Here we introduce a new software suite that is specifically designed for layer-specific functional MRI: LayNii. This toolbox is a collection of command-line executable programs written in C/C++ and is distributed opensource and as pre-compiled binaries for Linux, Windows, and macOS. LayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints and thus cannot be straightforwardly analyzed in alternative software packages. Some of the most popular programs of LayNii contain ‘layerification’ and columnarization in the native voxel space of functional data as well as many other layer-fMRI specific analysis tasks: layer-specific smoothing, model-based vein mitigation of GE-BOLD data, quality assessment of artifact dominated sub-millimeter fMRI, as well as analyses of VASO data. [Display omitted]
High-resolution fMRI in the sub-millimeter regime allows researchers to resolve brain activity across cortical layers and columns non-invasively. While these high-resolution data make it possible to address novel questions of directional information flow within and across brain circuits, the corresponding data analyses are challenged by MRI artifacts, including image blurring, image distortions, low SNR, and restricted coverage. These challenges often result in insufficient spatial accuracy of conventional analysis pipelines. Here we introduce a new software suite that is specifically designed for layer-specific functional MRI: LayNii. This toolbox is a collection of command-line executable programs written in C/C++ and is distributed opensource and as pre-compiled binaries for Linux, Windows, and macOS. LayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints and thus cannot be straightforwardly analyzed in alternative software packages. Some of the most popular programs of LayNii contain 'layerification' and columnarization in the native voxel space of functional data as well as many other layer-fMRI specific analysis tasks: layer-specific smoothing, model-based vein mitigation of GE-BOLD data, quality assessment of artifact dominated sub-millimeter fMRI, as well as analyses of VASO data.High-resolution fMRI in the sub-millimeter regime allows researchers to resolve brain activity across cortical layers and columns non-invasively. While these high-resolution data make it possible to address novel questions of directional information flow within and across brain circuits, the corresponding data analyses are challenged by MRI artifacts, including image blurring, image distortions, low SNR, and restricted coverage. These challenges often result in insufficient spatial accuracy of conventional analysis pipelines. Here we introduce a new software suite that is specifically designed for layer-specific functional MRI: LayNii. This toolbox is a collection of command-line executable programs written in C/C++ and is distributed opensource and as pre-compiled binaries for Linux, Windows, and macOS. LayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints and thus cannot be straightforwardly analyzed in alternative software packages. Some of the most popular programs of LayNii contain 'layerification' and columnarization in the native voxel space of functional data as well as many other layer-fMRI specific analysis tasks: layer-specific smoothing, model-based vein mitigation of GE-BOLD data, quality assessment of artifact dominated sub-millimeter fMRI, as well as analyses of VASO data.
ArticleNumber 118091
Author Huber, Laurentius (Renzo)
Reynolds, Richard C.
Arora, Kabir
Poser, Benedikt A.
Bandettini, Peter A.
Wagstyl, Konrad
Müller, Anna K
Glen, Daniel R.
Goense, Jozien
van den Hurk, Job
Nothnagel, Nils
Cho, Shinho
Morgan, Andrew Tyler
Goebel, Rainer
Gulban, Omer Faruk
AuthorAffiliation f Scannexus, Maastricht, the Netherlands
g Goethe University Frankfurt, Frankfurt, Germany
c Wellcome Centre for Human Neuroimaging, University College London, London, UK
b NIMH, NIH, Bethesda, MD, USA
e University of Glasgow, UK
a MBIC, Faculty of Psychology and Neuroscience, Maastricht University, the Netherlands
h Brain Innovation, Maastricht, the Netherlands
d CMRR, University of Minneapolis, MN, USA
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  organization: University of Glasgow, UK
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  surname: van den Hurk
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  surname: Gulban
  fullname: Gulban, Omer Faruk
  organization: MBIC, Faculty of Psychology and Neuroscience, Maastricht University, the Netherlands
BackLink https://www.ncbi.nlm.nih.gov/pubmed/33991698$$D View this record in MEDLINE/PubMed
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Snippet •A new software toolbox is introduced for layer-specific functional MRI: LayNii.•LayNii is a suite of command-line executable C++ programs for Linux, Windows,...
High-resolution fMRI in the sub-millimeter regime allows researchers to resolve brain activity across cortical layers and columns non-invasively. While these...
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SubjectTerms Accuracy
Brain - diagnostic imaging
Brain - physiology
Brain mapping
Brain research
Computer programs
Functional magnetic resonance imaging
Functional Neuroimaging - methods
Humans
Image Processing, Computer-Assisted - methods
Magnetic resonance imaging
Magnetic Resonance Imaging - methods
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