NEWS.md

In mandymejia/templateICAr: Estimate Brain Networks and Connectivity with ICA and Empirical Priors

10.0

• Delete plot_FC: it will be moved to fMRItools
• Delete src (locally) to have NeedsCompilation set to No.
• Delete diagnostic ICA scripts.

9.0

• Clean up dependencies
• Patch for dual_reg_parc

8.0

• Updates to template calculations
  • Use effective sample size
• Add prewhitening option to FC template ICA
• Implement rescaling to templateICA
• Default activation type is > rather than abs >

7.1

• use u and z for activtions, rather than gamma

7.0

• no PARDISO requirement
• correct package documentation
• adjustments to FC, VB
• add scrubbing

6.0

• activations: gray medial wall
• prep for adding FC template

5.0

?

4.0

estimate_template add custom smoothing add parallel over subjects

3.0

Fixes and cleaning up

2.0

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

1.2

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

1.0

• Package maintenance:

  • format DESCRIPTION
  • change import to importFrom where possible
  • add README.Rmd
  • add travis and appveyor
  • delete Rhistory
  • clean up gitignore & buildignore
  • add internal keyword to functions not exported
  • add titles to functions
  • some formatting to function descriptions
  • replace equal signs with arrows
  • add CITATION

• Only require INLA for spatial modeling.

mandymejia/templateICAr documentation built on June 2, 2025, 7:11 a.m.