Man pages for BayesBrainMap
Estimate Brain Networks and Connectivity with Population-Derived Priors
| add_str | Combine additive terms in string |
| bdiag_m | Block diagonal matrix |
| bdiag_m2 | Bdiag m2 |
| BrainMap | Bayesian brain mapping |
| check_parallel_packages | Check for required parallel packages |
| check_req_ifti_pkg | Check required packages for the data format |
| Chol_samp_fun | Cholesky-based FC sampling |
| compute_LL_std | Compute LL for EM Bayesian brain mapping |
| compute_mu_s | Compute posterior mean and precision of s |
| compute_R_inv | Compute SPDE and prior precision matrices for S |
| dim_reduce | PCA-based Dimension Reduction and Prewhitening |
| dual_reg2 | Dual Regression wrapper |
| EM_BrainMap | EM Algorithms for Bayesian brain maps |
| engagements | Engagements of (spatial) Bayesian brain mapping |
| estimate.ESS | Estimation of effective sample size |
| estimate_nu | Universally estimate IW dof parameter nu based on method of... |
| estimate_nu_matrix | Estimate IW dof parameter nu based on method of moments |
| estimate_prior | Estimate prior |
| estimate_prior_FC | Estimate FC prior |
| estimate_prior_from_DR | Estimate prior from DR |
| estimate_prior_from_DR_two | Estimate prior from DR estimates (when there are two... |
| export_prior | Export prior |
| format_engagement_name | Format engagement name |
| get_FORMAT | Get FORMAT from format |
| getInvCovAR | Compute inverse covariance matrix for AR process (up to a... |
| GSR_Param | GSR |
| halflogdetX | Half log determinant |
| hpf_param | hpf |
| INLA_check | Check for INLA |
| IW_var | Compute theoretical Inverse-Wishart variance of covariance... |
| IW_var_cor | Compute theoretical Inverse-Wishart variance of correlation... |
| lik | Compute likelihood in SPDE model for ESS estimation |
| LL2_kappa | Compute part of kappa log-likelihood |
| LL_SQUAREM | Log-likelihood SQUAREM |
| loglik_kappa_est | Kappa log-likelihood |
| make_mask | Create a mask based on vertices that are invalid |
| make_mesh | Make INLA mesh from '"surf"' object |
| make_mesh_2D | Make 2D INLA mesh |
| make_Pmat | Make permutation matrix |
| norm_BOLD | Normalize BOLD data |
| orthonorm | Orthonormalizes a square, invertible matrix |
| plot.bMap.cifti | Plot BrainMap estiamte |
| plot.bMap_eng.cifti | Plot engagements |
| plot.bMap.matrix | Plot prior |
| plot.bMap.nifti | Plot prior |
| plot.prior.cifti | Plot prior |
| plot.prior.gifti | Plot prior |
| plot.prior.matrix | Plot prior |
| plot.prior.nifti | Plot prior |
| pw_estimate | Estimate residual autocorrelation for prewhitening |
| Q2_max_check | Check 'Q2_max' |
| removebs_prior | Remove brain structure from CIFTI prior |
| resample_prior | Resample CIFTI prior |
| rm_nuisIC | Remove nuisance ICs from data |
| scale_Param | scale |
| sqrt_XtX | Compute matrix square root of X'X |
| struct_prior | Apply data structure to priors |
| summary.bMap.cifti | Summarize a '"bMap.cifti"' object |
| summary.bMap_eng.cifti | Summarize a '"bMap_eng.cifti"' object |
| summary.bMap_eng.matrix | Summarize a '"bMap_eng.matrix"' object |
| summary.bMap_eng.nifti | Summarize a '"bMap_eng.nifti"' object |
| summary.bMap.matrix | Summarize a '"bMap.matrix"' object |
| summary.bMap.nifti | Summarize a '"bMap.nifti"' object |
| summary.prior.cifti | Summarize a '"prior.cifti"' object |
| summary.prior.gifti | Summarize a '"prior.gifti"' object |
| summary.prior.matrix | Summarize a '"prior.matrix"' object |
| summary.prior.nifti | Summarize a '"prior.nifti"' object |
| TR_param | TR |
| update_A | Update A for VB FC Bayesian brain mapping using IW prior on... |
| update_A_Chol | Update A for VB FC Bayesian brain mapping using Cholesky... |
| update_S | Update S for VB FC Bayesian brain mapping |
| update_tau2 | Update tau for VB FC Bayesian brain mapping |
| UpdateTheta_BrainMap | Parameter Estimates in EM Algorithm for Bayesian brain map |
| UpdateThetaSQUAREM_BrainMap | Update theta SQUAREM |
| var_sq_err | Compute the error between empirical and theoretical variance... |
| var_sq_err_constrained | Compute the overall error between empirical and theoretical... |
| varTol_Param | varTol |
| VB_FCBrainMap | VB_FCBrainMap |
