Rapidtide

Rapidtide is a suite of python programs used to perform rapid time delay analysis on functional imaging data to find time lagged correlations between the voxelwise time series and other time series, both in the LFO band (rapditide2) and now in the cardiac band (happy).

Citing rapidtide

Frederick, B, rapidtide [Computer Software] (2016-2022). Available from https://github.com/bbfrederick/rapidtide. doi:10.5281/zenodo.814990

Contents

Introduction:

• The rapidtide package
  • The rapidtide program
    • Why do I want to know about time lagged correlations?
    • Correlation analysis is easy - why use this package?
  • Happy
    • What does "happy" have to do with any of this?
• Why are you releasing this package?
• Stability, etc.
• Python version compatibility
• Ok, I'm sold. What's in here?
• Financial Support
• Additional packages used
  • numpy:
  • scipy:
  • matplotlib:
  • nibabel:
  • scikit-learn:
  • pandas:
  • nilearn:
• References
  • General overview of systemic low frequency oscillations in fMRI data
  • Multimodal Cerebral Circulation Imaging
  • Cardiac waveform extraction and refinement
  • Physiological noise identification and removal using time delay methods

Installation:

• Bare metal installation
  • Required dependencies
  • Optional dependencies
  • Installing Python
  • Installing the rapidtide library
  • Updating
• Docker installation
• Singularity installation
• References

Usage:

• Background
  • BIDS Outputs
  • Text Inputs
  • Visualizing files
• rapidtide
  • Description:
  • Inputs:
  • Outputs:
  • BIDS Outputs:
  • Usage:
  • Legacy interface:
  • Equivalence between BIDS and legacy outputs:
  • Examples:
• happy
  • Description:
  • Inputs:
  • Outputs:
  • BIDS Outputs:
  • Usage:
  • Example:
• rapidtide2std
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• showxcorr_legacy
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• showxcorrx
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• showtc
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• glmfilt
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• temporaldecomp
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• spatialdecomp
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• polyfitim
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• histnifti
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• showhist
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• resamp1tc
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• resamplenifti
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• tcfrom3col
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• pixelcomp
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• glmfilt
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• ccorrica
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• showstxcorr
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• tidepool
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• API
  • rapidtide.workflows: Rapidtide workflows
  • rapidtide.correlate: Correlation functions
  • rapidtide.filter: Filters
  • rapidtide.fit: Fitting functions
  • rapidtide.io: Input/output functions
  • rapidtide.miscmath: Miscellaneous math functions
  • rapidtide.resample: Resampling functions
  • rapidtide.stats: Statistical functions
  • rapidtide.util: Utility functions
• Contributing to rapidtide
  • Style Guide
  • A note on current coding quality and style

Digging deeper:

• Theory of operation
  • rapidtide

History:

• Release history
  • Version 2.5.7 (5/15/23)
  • Version 2.5.6 (5/14/23)
  • Version 2.5.5 (5/11/23)
  • Version 2.5.4 (5/10/23)
  • Version 2.5.3.1 (5/9/23)
  • Version 2.5.3 (5/9/23)
  • Version 2.5.2 (5/8/23)
  • Version 2.5.1.2 (4/28/23)
  • Version 2.5.1.1 (4/28/23)
  • Version 2.5.1 (4/28/23)
  • Version 2.5 (4/28/23)
  • Version 2.4.5.1 (4/10/23)
  • Version 2.4.5 (4/10/23)
  • Version 2.4.4 (3/30/23)
  • Version 2.4.3 (3/30/23)
  • Version 2.4.2 (2/8/23)
  • Version 2.4.1 (10/12/22)
  • Version 2.4.0 (10/6/22)
  • Version 2.3.1 (9/27/22)
  • Version 2.3.0 (9/23/22)
  • Version 2.2.9 (9/21/22)
  • Version 2.2.8.1 (8/29/22)
  • Version 2.2.8 (8/29/22)
  • Version 2.2.7.1 (6/30/22)
  • Version 2.2.7 (6/29/22)
  • Version 2.2.6 (5/17/22)
  • Version 2.2.5 (4/26/22)
  • Version 2.2.4 (4/11/22)
  • Version 2.2.3 (4/1/22)
  • Version 2.2.2 (3/16/22)
  • Version 2.2.1 (3/16/22)
  • Version 2.2.0 (3/11/22)
  • Version 2.1.2 (1/10/22)
  • Version 2.1.1 (11/4/21)
  • Version 2.1.0 (9/21/21)
  • Version 2.0.9 (8/26/21)
  • Version 2.0.8 (8/20/21)
  • Version 2.0.7 (8/19/21)
  • Version 2.0.6 (8/16/21)
  • Version 2.0.5 (8/9/21)
  • Version 2.0.4 (7/28/21)
  • Version 2.0.3 (7/16/21)
  • Version 2.0.2 (6/10/21)
  • Version 2.0.1 (6/8/21)
  • Version 2.0 (6/2/21)
  • Version 2.0alpha29 (6/1/21)
  • Version 1.9.6 (6/1/21)
  • Version 2.0alpha28 (5/27/21)
  • Version 1.9.5 (5/27/21)
  • Version 2.0alpha27 (5/27/21)
  • Version 2.0alpha26 (5/5/21)
  • Version 2.0alpha25 (5/3/21)
  • Version 2.0alpha24 (4/14/21)
  • Version 2.0alpha23 (4/14/21)
  • Version 2.0alpha22 (4/13/21)
  • Version 2.0alpha21 (4/12/21)
  • Version 2.0alpha20 (3/28/21)
  • Version 2.0alpha19 (3/26/21)
  • Version 2.0alpha18 (3/17/21)
  • Version 1.9.4 (3/17/21)
  • Version 2.0alpha17 (3/17/21)
  • Version 2.0alpha16 (3/17/21)
  • Version 2.0alpha15 (3/17/21)
  • Version 2.0alpha14 (3/1/21)
  • Version 2.0alpha13 (2/22/21)
  • Version 2.0alpha12 (2/5/21)
  • Version 2.0alpha11 (1/5/21)
  • Version 2.0alpha10 (12/21/20)
  • Version 2.0alpha9 (12/9/20)
  • Version 2.0alpha8 (12/9/20)
  • Version 2.0alpha7 (12/1/20)
  • Version 2.0alpha6 (11/30/20)
  • Version 2.0alpha5 (10/29/20)
  • Version 2.0alpha4 (10/26/20)
  • Version 2.0alpha3 (10/19/20)
  • Version 2.0alpha2 (10/19/20)
  • Version 2.0alpha1 (8/24/20)
  • Version 1.9.3 (7/30/20)
  • Version 1.9.2 (7/30/20)
  • Version 1.9.1 (6/17/20)
  • Version 1.9 (1/6/20)
  • Version 1.8 (5/10/19)
  • Version 1.7 (12/5/18)
  • Version 1.6 (9/19/18)
  • Version 1.5 (6/11/18)
  • Version 1.4.2 (2/21/18)
  • Version 1.4.0 (2/21/18)
  • Version 1.3.0 (12/15/17)
  • Version 1.2.0 (6/20/17)
  • Version 1.1.0 (4/3/17)
  • Version 1.0.0 (2/13/17)
  • Version 0.1.9 (12/19/16)
  • Version 0.1.8 (11/30/16)
  • Version 0.1.7 (11/15/16)
  • Version 0.1.6 (10/15/16)
  • Version 0.1.5 (10/11/16)
  • Version 0.1.4 (10/10/16)
  • Version 0.1.3 (9/2/16)
  • Version 0.1.2 (8/5/16)
  • Version 0.1.1 (7/8/16)
  • Version 1.3.0 (12/15/17)
  • Version 1.2.0 (6/20/17)
  • Version 1.1.0 (4/3/17)
  • Version 1.0.0 (2/13/17)
  • Version 0.1.9 (12/19/16)
  • Version 0.1.8 (11/30/16)
  • Version 0.1.7 (11/15/16)
  • Version 0.1.6 (10/15/16)
  • Version 0.1.5 (10/11/16)
  • Version 0.1.4 (10/10/16)
  • Version 0.1.3 (9/2/16)
  • Version 0.1.2 (8/5/16)
  • Version 0.1.1 (7/8/16)

Indices and tables

• Index

• Module Index

• Search Page