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  "Title": "Estimate Brain Networks and Connectivity with ICA and Empirical\nPriors",
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  "Description": "Implements the template ICA (independent components\nanalysis) model proposed in Mejia et al. (2020)\n<doi:10.1080/01621459.2019.1679638> and the spatial template\nICA model proposed in proposed in Mejia et al. (2022)\n<doi:10.1080/10618600.2022.2104289>. Both models estimate\nsubject-level brain as deviations from known population-level\nnetworks, which are estimated using standard ICA algorithms.\nBoth models employ an expectation-maximization algorithm for\nestimation of the latent brain networks and unknown model\nparameters. Includes direct support for 'CIFTI', 'GIFTI', and\n'NIFTI' neuroimaging file formats.",
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  "Repository": "https://mandymejia.r-universe.dev",
  "Date/Publication": "2025-05-20 19:12:51 UTC",
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    "groupICA.cifti",
    "make_mesh",
    "make_mesh_2D",
    "norm_BOLD",
    "orthonorm",
    "resample_template",
    "sqrt_XtX",
    "templateICA"
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      "page": "activations",
      "title": "Activations of (spatial) template ICA",
      "topics": [
        "activations"
      ]
    },
    {
      "page": "bdiag_m2",
      "title": "Bdiag m2",
      "topics": [
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    },
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      "page": "Chol_samp_fun",
      "title": "Cholesky-based FC sampling",
      "topics": [
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      ]
    },
    {
      "page": "dim_reduce",
      "title": "PCA-based Dimension Reduction and Prewhitening",
      "topics": [
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      ]
    },
    {
      "page": "EM_templateICA",
      "title": "EM Algorithms for Template ICA Models",
      "topics": [
        "EM_templateICA",
        "EM_templateICA.independent",
        "EM_templateICA.spatial"
      ]
    },
    {
      "page": "estimate_nu",
      "title": "Universally estimate IW dof parameter nu based on method of moments, so that no empirical variance is under-estimated",
      "topics": [
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      ]
    },
    {
      "page": "estimate_nu_matrix",
      "title": "Estimate IW dof parameter nu based on method of moments",
      "topics": [
        "estimate_nu_matrix"
      ]
    },
    {
      "page": "estimate_template",
      "title": "Estimate template",
      "topics": [
        "estimate_template",
        "estimate_template.cifti",
        "estimate_template.gifti",
        "estimate_template.nifti"
      ]
    },
    {
      "page": "estimate_template_FC",
      "title": "Estimate FC template",
      "topics": [
        "estimate_template_FC"
      ]
    },
    {
      "page": "estimate_template_from_DR",
      "title": "Estimate template from DR",
      "topics": [
        "estimate_template_from_DR"
      ]
    },
    {
      "page": "estimate.ESS",
      "title": "Estimation of effective sample size",
      "topics": [
        "estimate.ESS"
      ]
    },
    {
      "page": "export_template",
      "title": "Export template",
      "topics": [
        "export_template"
      ]
    },
    {
      "page": "getInvCovAR",
      "title": "Compute inverse covariance matrix for AR process (up to a constant scaling factor)",
      "topics": [
        "getInvCovAR"
      ]
    },
    {
      "page": "groupICA.cifti",
      "title": "Perform group ICA based on CIFTI data",
      "topics": [
        "groupICA.cifti"
      ]
    },
    {
      "page": "IW_var",
      "title": "Compute theoretical Inverse-Wishart variance of covariance matrix elements",
      "topics": [
        "IW_var"
      ]
    },
    {
      "page": "IW_var_cor",
      "title": "Compute theoretical Inverse-Wishart variance of correlation matrix elements",
      "topics": [
        "IW_var_cor"
      ]
    },
    {
      "page": "lik",
      "title": "Compute likelihood in SPDE model for ESS estimation",
      "topics": [
        "lik"
      ]
    },
    {
      "page": "make_mesh",
      "title": "Make INLA mesh from '\"surf\"' object",
      "topics": [
        "make_mesh"
      ]
    },
    {
      "page": "make_mesh_2D",
      "title": "Make 2D INLA mesh",
      "topics": [
        "make_mesh_2D"
      ]
    },
    {
      "page": "norm_BOLD",
      "title": "Normalize BOLD data",
      "topics": [
        "norm_BOLD"
      ]
    },
    {
      "page": "orthonorm",
      "title": "Orthonormalizes a square, invertible matrix",
      "topics": [
        "orthonorm"
      ]
    },
    {
      "page": "plot.template.cifti",
      "title": "Plot template",
      "topics": [
        "plot.template.cifti"
      ]
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    {
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      "title": "Plot template",
      "topics": [
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      "page": "plot.template.matrix",
      "title": "Plot template",
      "topics": [
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      ]
    },
    {
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      "title": "Plot template",
      "topics": [
        "plot.template.nifti"
      ]
    },
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      "title": "Plot activations",
      "topics": [
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    },
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      "title": "Plot template",
      "topics": [
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      ]
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      "title": "Plot template",
      "topics": [
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      ]
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      "title": "Plot template",
      "topics": [
        "plot.tICA.nifti"
      ]
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    {
      "page": "pw_estimate",
      "title": "Estimate residual autocorrelation for prewhitening",
      "topics": [
        "pw_estimate"
      ]
    },
    {
      "page": "resample_template",
      "title": "Resample CIFTI template",
      "topics": [
        "resample_template"
      ]
    },
    {
      "page": "sqrt_XtX",
      "title": "Compute matrix square root of X'X",
      "topics": [
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    },
    {
      "page": "summary.template.cifti",
      "title": "Summarize a '\"template.cifti\"' object",
      "topics": [
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        "print.template.cifti",
        "summary.template.cifti"
      ]
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        "print.template.gifti",
        "summary.template.gifti"
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      "title": "Summarize a '\"template.matrix\"' object",
      "topics": [
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        "print.template.matrix",
        "summary.template.matrix"
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    },
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      "topics": [
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        "print.template.nifti",
        "summary.template.nifti"
      ]
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      "title": "Summarize a '\"tICA_act.cifti\"' object",
      "topics": [
        "print.summary.tICA_act.cifti",
        "print.tICA_act.cifti",
        "summary.tICA_act.cifti"
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    },
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      "title": "Summarize a '\"tICA_act.matrix\"' object",
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        "print.tICA_act.matrix",
        "summary.tICA_act.matrix"
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      "title": "Summarize a '\"tICA_act.nifti\"' object",
      "topics": [
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        "print.tICA_act.nifti",
        "summary.tICA_act.nifti"
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      "topics": [
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        "print.tICA.matrix",
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        "summary.tICA.nifti"
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      "topics": [
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        "UpdateTheta_templateICA.spatial"
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    },
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      "title": "Compute the overall error between empirical and theoretical variance of CORRELATION matrix elements",
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