estimate_template * add custom smoothing * add parallel over subjects


Fixes and cleaning up


Data pre-processing, for both template estimation and TemplateICA * norm_BOLD replaces scale_BOLD, since now it detrends the data too. * Do not scale across space by default. Instead, scale across space only where necessary (one of the regressions in dual regression, and PCA-based operations). * Option to detrend. * Compute scale after centering and detrending.

Dual regression * Option to normalize A matrix

Template estimation * Merge estimate_template.cifti and estimate_template.nifti into estimate_template * Option to denoise each scan before computing DR * If using pseudo retest data, split each subject’s scan after denoising and detrending, not before. * Option for different variance template (non-negative) * Option to obtain DR results * Return parameters, including data normalization choices. * print and summary for templates

TemplateICA * Merge templateICA.cifti and templateICA.nifti into templateICA * Option to return DR results in estimate_template * Option to skip dimension reduction * Option to use parallel computing for iterating over voxels. * Option to provide "xifti" or "nifti" objects directly * Option to provide multiple scans * For denoising: replace maxQ with Q2_max to simplify logic * Fix cases where time_inds and resamp_res are provided. * Return parameters, including data normalization choices. * Replace subject IC variance with the standard error * summary and plot for activations

Misc * Implement sign matching * Refine group_ICA * Refine make_mesh * Remove INLA required version (bring back?)

For developers * Laid some groundwork for estimating templates using >2 scans per subject: var_decomp can handle >2 scans per subject (but need to test it!) * New code template calculation


Update functions that work with "xifti" objects to conserve time and memory.