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bioRxiv · 10.1101/2020.06.12.148080

LAYNII: A software suite for layer-fMRI

Huber, L.·Poser, B. A.·Bandettini, P. A.·Arora, K.·Wagstyl, K.·Cho, S.·Goense, J.·Nothnagel, N.·Morgan, A. T.·van den Hurk, J.·Reynolds, R. C.·Glen, D. R.·Goebel, R. W.·Gulban, O. F.
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Abstract

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 open-source 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. HighlightsO_LIA new software toolbox is introduced for layer-specific functional MRI: LayNii. C_LIO_LILayNii is a suite of command-line executable C++ programs for Linux, Windows, and macOS. C_LIO_LILayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints. C_LIO_LILayNii performs layerification in the native voxel space of functional data. C_LIO_LILayNii performs layer-smoothing, GE-BOLD deveining, QA, and VASO analysis. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/148080v3_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@e12e9org.highwire.dtl.DTLVardef@1fbb564org.highwire.dtl.DTLVardef@41da13org.highwire.dtl.DTLVardef@1545106_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

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Huber, L., Poser, B. A., Bandettini, P. A., Arora, K., Wagstyl, K., Cho, S., Goense, J., Nothnagel, N., Morgan, A. T., van den Hurk, J., Reynolds, R. C., Glen, D. R., Goebel, R. W., Gulban, O. F.. 2020-06-14. LAYNII: A software suite for layer-fMRI. https://doi.org/10.1101/2020.06.12.148080

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