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
- General points
- rapidtide
- Description:
- Inputs:
- Outputs:
- BIDS Outputs:
- Usage:
- Positional Arguments
- Analysis type
- Macros
- Preprocessing options
- Filtering options
- Significance calculation options
- Windowing options
- Correlation options
- Correlation fitting options
- Regressor refinement options
- GLM noise removal options
- Output options
- Version options
- Performance options
- Miscellaneous options
- Experimental options (not fully tested, may not work)
- 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
- Analysis Examples:
- rapidtide2std
- tidepool
- adjustoffset
- 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
- Output options
- Phase projection tuning
- Version options
- Miscellaneous options.
- Debugging options (probably not of interest to users)
- Example:
- happy2std
- proj2flow
- showxcorr_legacy
- showxcorrx
- showtc
- showxy
- showhist
- spectrogram
- glmfilt
- atlasaverage
- ccorrica
- tcfrom2col
- tcfrom3col
- pixelcomp
- atlastool
- applydlfilter
- calctexticc
- diffrois
- endtidalproc
- filtnifti
- filttc
- histtc
- histnifti
- resamplenifti
- resampletc
- aligntcs
- temporaldecomp
- spatialdecomp
- polyfitim
- mergequality
- pairproc
- pairwisemergenifti
- physiofreq
- plethquality
- rankimage
- runqualitycheck
- variabilityizer
- fdica
- gmscalc
- roisummarize
- simdata
- spatialfit
- spatialmi
- localflow
- synthASL
- Legacy interface:
- Equivalence between BIDS and legacy outputs:
- API
- Contributing to rapidtide
- Theory of operation
- rapidtide
- 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
- Regress Out the Moving Signal
- References
- Release history
- Version 2.8.8 (4/30/24)
- Version 2.8.7 (4/17/24)
- Version 2.8.6 (4/5/24)
- Version 2.8.5.1 (4/1/24)
- Version 2.8.5 (3/30/24)
- Version 2.8.4 (3/28/24)
- Version 2.8.3 (3/7/24)
- Version 2.8.2 (2/26/24)
- Version 2.8.1 (2/19/24)
- Version 2.8.0 (2/18/24)
- Version 2.7.9 (2/18/24)
- Version 2.7.8 (1/31/24)
- Version 2.7.7 (1/31/24)
- Version 2.7.6 (1/29/24)
- Version 2.7.5 (1/13/24)
- Version 2.7.4 (1/10/24)
- Version 2.7.3.3 (12/18/23)
- Version 2.7.3.2 (12/18/23)
- Version 2.7.3.1 (12/18/23)
- Version 2.7.3 (12/18/23)
- Version 2.7.2 (12/12/23)
- Version 2.7.1 (12/12/23)
- Version 2.7.0 (12/11/23)
- Version 2.6.9.1 (12/11/23)
- Version 2.6.9 (12/11/23)
- Version 2.6.8 (11/21/23)
- Version 2.6.7 (10/31/23)
- Version 2.6.6 (10/7/23)
- Version 2.6.5 (10/4/23)
- Version 2.6.4 (9/28/23)
- Version 2.6.3 (9/13/23)
- Version 2.6.2 (8/29/23)
- Version 2.6.1 (8/17/23)
- Version 2.6.0 (8/10/23)
- Version 2.5.8 (8/3/23)
- 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)