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] (2016-2024). 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.
• Testing lanes
• Python version compatibility
• Ok, I'm sold. What's in here?
• Financial Support
• Additional packages used
  • numpy:
  • scipy:
  • matplotlib:
  • nibabel:
  • scikit-image:
  • scikit-learn:
  • statsmodels:
  • pandas:
  • nilearn:
  • pyqtgraph:
• 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 with pip from pypi
  • Installing from Github
• Docker installation
• Singularity installation
• References
• Support and communication

Usage:

• General points
  • Standardization of interfaces
  • BIDS Outputs
  • Text Inputs
    • A plain text file with one or more columns.
    • A BIDS continuous file with one or more columns.
  • Visualizing files
• rapidtide
  • Description:
  • Inputs:
  • Outputs:
  • BIDS Outputs:
  • Output data size:
  • Usage:
    • Positional Arguments
    • Analysis type
    • Macros
    • Anatomic information
    • Preprocessing options
    • Filtering options
    • Significance calculation options
    • Windowing options
    • Correlation options
    • Correlation fitting options
    • Regressor refinement options
    • sLFO noise removal options
    • Output options
    • Version options
    • Performance options
    • Miscellaneous options
    • Experimental options (not fully tested, or not tested at all, may not work). Beware!
    • Deprecated options. These options will go away in the indeterminate future. Don’t use them.
    • Debugging options. You probably don’t want to use any of these unless I ask you to to help diagnose a problem
  • Preprocessing for rapidtide
    • Working with standard fMRI packages
  • Analysis Examples:
    • Removing low frequency physiological noise from fMRI data
    • Removing low frequency physiological noise from fMRI data that has been processed with FIX
    • Mapping long time delays in response to a gas challenge experiment:
    • Getting an initial regressor from the Superior Sagittal Sinus (SSS)
    • CVR mapping:
    • Denoising NIRS data:
    • Can I use this for other frequency ranges?:
  • References
• rapidtide2std
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• tidepool
  • Description:
  • Inputs:
  • Features:
    • Image Data
    • Overlay Selector
    • Information panel
    • Histogram
    • Similarity Function
    • Probe Regressor
    • Dataset selection
  • Usage:
    • Named Arguments
• adjustoffset
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
    • Masking options
• happy
  • Description:
  • Inputs:
  • Outputs:
  • BIDS Outputs:
  • Usage:
    • Positional Arguments
    • Processing steps
    • Performance
    • Preprocessing
    • Cardiac estimation tuning
    • External cardiac waveform options
    • External respiration waveform options
    • Output processing - mutually exclusive options
    • Output options
    • Phase projection tuning
    • Version options
    • Miscellaneous options.
    • Debugging options (probably not of interest to users)
  • Example:
    • Extract the cardiac waveform and generate phase projections
  • References
• happy2std
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• proj2flow
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• showxcorr_legacy
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
• showxcorrx
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • General Options
    • Windowing options
    • Filtering options
    • Preprocessing options
    • Additional calculations
    • Significance calculation options
    • Similarity function options
    • Output options
    • General plot appearance options
    • Miscellaneous options
    • Debugging options
• showtc
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
    • General plot appearance options
    • Version options
• showxy
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• showhist
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• spectrogram
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• linfitfilt
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• atlasaverage
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• ccorrica
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
    • Windowing options
    • Filtering options
• tcfrom2col
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• tcfrom3col
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• pixelcomp
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• atlastool
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• applydlfilter
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• calctexticc
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• diffrois
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• endtidalproc
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• filtnifti
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• filttc
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
    • Filtering options
    • Normalization options
• histtc
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• histnifti
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• resamplenifti
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• resampletc
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• aligntcs
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
    • Filtering options
• temporaldecomp
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• spatialdecomp
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• polyfitim
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• mergequality
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Named Arguments
• pairproc
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• pairwisemergenifti
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• physiofreq
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• plethquality
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• rankimage
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• runqualitycheck
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• variabilityizer
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
• fdica
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• gmscalc
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
    • Normalization options
• roisummarize
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
    • Filtering options
    • Normalization options
• simdata
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
    • LFO band options
    • Resp band options
    • Cardiac band options
• spatialfit
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• spatialmi
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• localflow
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
    • Filtering options
    • Windowing options
    • Miscellaneous options
• synthASL
  • Description:
  • Inputs:
  • Outputs:
  • Usage:
    • Positional Arguments
    • Named Arguments
• Legacy interface:
• Equivalence between BIDS and legacy outputs:
• API
  • rapidtide
• Contributing to rapidtide
  • Style Guide
    • Code
    • Pull Requests
  • A note on current coding quality and style

Digging deeper:

• Theory of operation
  • What is rapidtide trying to do?
  • What is the difference between RIPTiDe and rapidtide?
  • How does rapidtide work?
    • Generation of Masks
    • Initial Moving Signal Estimation
    • Moving Signal Preprocessing
    • Moving Signal Massaging
    • Dataset Preprocessing
    • Significance threshold estimation
    • Time delay determination
    • Generating a better moving signal estimate (refinement)
    • Lather, Rinse, Repeat
    • Delay Refinement
    • Regress Out the Moving Signal
    • References

History:

• What's new
  • Version 3.0 summary:
• Individual releases:
  • Release history

Indices and tables

• Index

• Module Index

• Search Page