LayNii: A software suite for layer-fMRI
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 corresp...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2021-08-01
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| Series: | NeuroImage |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1053811921003682 |
| _version_ | 1818621965139705856 |
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| author | Laurentius (Renzo) Huber Benedikt A. Poser Peter A. Bandettini Kabir Arora Konrad Wagstyl Shinho Cho Jozien Goense Nils Nothnagel Andrew Tyler Morgan Job van den Hurk Anna K Müller Richard C. Reynolds Daniel R. Glen Rainer Goebel Omer Faruk Gulban |
| author_facet | Laurentius (Renzo) Huber Benedikt A. Poser Peter A. Bandettini Kabir Arora Konrad Wagstyl Shinho Cho Jozien Goense Nils Nothnagel Andrew Tyler Morgan Job van den Hurk Anna K Müller Richard C. Reynolds Daniel R. Glen Rainer Goebel Omer Faruk Gulban |
| author_sort | Laurentius (Renzo) Huber |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-16T18:17:39Z |
| format | Article |
| id | doaj.art-af11e955ff2346acb47332512ef5d0ec |
| institution | Directory Open Access Journal |
| issn | 1095-9572 |
| language | English |
| last_indexed | 2024-12-16T18:17:39Z |
| publishDate | 2021-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | NeuroImage |
| spelling | doaj.art-af11e955ff2346acb47332512ef5d0ec2022-12-21T22:21:39ZengElsevierNeuroImage1095-95722021-08-01237118091LayNii: A software suite for layer-fMRILaurentius (Renzo) Huber0Benedikt A. Poser1Peter A. Bandettini2Kabir Arora3Konrad Wagstyl4Shinho Cho5Jozien Goense6Nils Nothnagel7Andrew Tyler Morgan8Job van den Hurk9Anna K Müller10Richard C. Reynolds11Daniel R. Glen12Rainer Goebel13Omer Faruk Gulban14MBIC, Faculty of Psychology and Neuroscience, Maastricht University, the Netherlands; Corresponding author.MBIC, Faculty of Psychology and Neuroscience, Maastricht University, the NetherlandsNIMH, NIH, Bethesda, MD, USAMBIC, Faculty of Psychology and Neuroscience, Maastricht University, the NetherlandsWellcome Centre for Human Neuroimaging, University College London, London, UKCMRR, University of Minneapolis, MN, USAUniversity of Glasgow, UKUniversity of Glasgow, UKUniversity of Glasgow, UKScannexus, Maastricht, the NetherlandsGoethe University Frankfurt, Frankfurt, GermanyNIMH, NIH, Bethesda, MD, USANIMH, NIH, Bethesda, MD, USAMBIC, Faculty of Psychology and Neuroscience, Maastricht University, the Netherlands; Brain Innovation, Maastricht, the NetherlandsMBIC, Faculty of Psychology and Neuroscience, Maastricht University, the Netherlands; Brain Innovation, Maastricht, the NetherlandsHigh-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.http://www.sciencedirect.com/science/article/pii/S1053811921003682 |
| spellingShingle | Laurentius (Renzo) Huber Benedikt A. Poser Peter A. Bandettini Kabir Arora Konrad Wagstyl Shinho Cho Jozien Goense Nils Nothnagel Andrew Tyler Morgan Job van den Hurk Anna K Müller Richard C. Reynolds Daniel R. Glen Rainer Goebel Omer Faruk Gulban LayNii: A software suite for layer-fMRI NeuroImage |
| title | LayNii: A software suite for layer-fMRI |
| title_full | LayNii: A software suite for layer-fMRI |
| title_fullStr | LayNii: A software suite for layer-fMRI |
| title_full_unstemmed | LayNii: A software suite for layer-fMRI |
| title_short | LayNii: A software suite for layer-fMRI |
| title_sort | laynii a software suite for layer fmri |
| url | http://www.sciencedirect.com/science/article/pii/S1053811921003682 |
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