NEWS

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templateICAr 9.0

• Clean up dependencies
• Patch for dual_reg_parc

templateICAr 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 >

templateICAr 7.1

• use u and z for activtions, rather than gamma

templateICAr 7.0

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

templateICAr 6.0

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

templateICAr 5.0

?

templateICAr 4.0

estimate_template

• add custom smoothing
• add parallel over subjects

templateICAr 3.0

Fixes and cleaning up

templateICAr 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

templateICAr 1.2

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

templateICAr 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.