Rapidtide is a suite of Python programs used to model, characterize, visualize, and remove time varying, physiological blood signals from fMRI and fNIRS datasets. The primary workhorses of the package are the rapidtide program, which characterizes bulk blood flow, and happy, which focusses on the cardiac band.

Reference:

• Yunjie Tong, Lia M. Hocke and Blaise B. Frederick, Low Frequency Systemic Hemodynamic “Noise” in Resting State BOLD fMRI: Characteristics, Causes, Implications, Mitigation Strategies, and Applications
  Frontieres in Neuroscience, 13, Article 787 (2019).
  Documentation
  • rapidtide Github page
  • rapidtide Documentation
  Important Notes
  • Module Name: rapidtide (see the modules page for more information)
  • Unusual environment variables set
    • RFRT_HOME  installation directory
    • RFRT_BIN       executable directory
    • RFRT_SRC       source code directory
    • RFRT_DATA  sample data directory
  Interactive job
  Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

  Allocate an interactive session and run the program. Sample session:

  [user@biowulf]$ sinteractive
  [user@cn3335 ~]$ module load rapidtide 
  [+] Loading singularity  4.0.1  on cn3335
  [+] Loading rapidtide  2.8.2
  

  Available executables:

  [user@cn3335 ~]$ ls $RT_BIN
  ccorrica  happy      polyfitim  rapidtide2std  resamplenifti  showhist     showtc      spatialdecomp  temporaldecomp
  glmfilt   histnifti  rapidtide  resamp1tc      shell          showstxcorr  showxcorrx  tcfrom3col     tidepool
  

  Usage:

  [user@cn3335 ~]$ rapidtide -h
  ...
  [user@cn3335 ~]$ happy -h 
  ...
  

  etc.
  Running an example:

  [user@cn3335 ~]$ git clone https://github.com/bbfrederick/rapidtide
  [user@cn3335 ~]$ cd rapidtide
  [user@cn3335 ~]$ happy rapidtide/data/examples/databundle/sub-HAPPYTEST.nii.gz \
                            rapidtide/data/examples/databundle/sub-HAPPYTEST.json \
                            rapidtide/data/examples/testdatabundle.tgz
  ...
  processing command line arguments
  running version 2.8.3+31.gbdf5c539 on host cn2895
  tr is 1.16 seconds, mrsamplerate is 0.862
  projmask has 112685 voxels above threshold.
  Normalizing voxels...
  Detrending to order 3 ...
  Voxel: 100%|██████████████████████████████████████████████████████████████████| 112685/112685 [00:09<00:00, 12367.61voxels/s]
   done
  Normalization took 10.458 seconds
  Not using separate estimation mask - doing initial estimate using intensity mask
  estmask has 112685 voxels above threshold.
  
  
  starting pass 1 of 2
  estimating cardiac signal from fmri data
  64 slice times with 16 unique values - diff is 0.073
  Making slice means...
  Averaging slices...
  done
  Slice sample rate is  13.793
  Notch filtering...
  Bad point threshhold set to 3.015 using the mad method for cardfromfmri_sliceres
  extracting harmonic components
  Filtering
  Envelope detection
  Normalizing
  Bad point threshhold set to 3.015 using the mad method for cardfromfmri_25.0Hz
  dlfilter could not be loaded - skipping
  entering phaseanalysis
  Filtering phase waveform
  Starting phase projection
  lookaheadval =  3
  Phase projecting...
  Slice: 100%|█████████████████████████████████████████████████████████████████████████████| 64/64 [00:13<00:00,  4.73slices/s]
   done
  Phase projection done
  hard, soft vessel threshholds set to 990.509 396.204
  
  
  starting pass 2 of 2
  estimating cardiac signal from fmri data
  64 slice times with 16 unique values - diff is 0.073
  Making slice means...
  Averaging slices...
  done
  Slice sample rate is  13.793
  Notch filtering...
  Bad point threshhold set to 3.015 using the mad method for cardfromfmri_sliceres
  extracting harmonic components
  Filtering
  Envelope detection
  Normalizing
  Bad point threshhold set to 3.015 using the mad method for cardfromfmri_25.0Hz
  dlfilter could not be loaded - skipping
  entering phaseanalysis
  Filtering phase waveform
  Starting phase projection
  lookaheadval =  3
  Phase projecting...
  Slice: 100%|█████████████████████████████████████████████████████████████████████████████| 64/64 [00:12<00:00,  5.12slices/s]
   done
  Phase projection done
  hard, soft vessel threshholds set to 1399.694 559.878
  Processed on cn2895
  Clock time      Program time    Duration        Description
  20240326T115909      0.00             0.00      Start
  20240326T115909      0.01             0.01      Argument parsing done
  20240326T115909      0.03             0.03      Argument parsing done
  20240326T115909      0.69             0.65      Image data read in
  20240326T115910      1.59             0.91      Mask created
  20240326T115910      1.61             0.01      Mask saved
  20240326T115910      1.61             0.00      Slice times determined
  20240326T115919     10.80             9.20      Detrending finished (40265.22 voxels/second)
  20240326T115921     12.15             1.34      Normalization finished (275338.63 voxels/second)
  20240326T115921     12.39             0.24      Cardiac signal generated from image data - pass 1
  20240326T115921     12.41             0.03      Cardiac signal from image data analyzed - pass 1
  20240326T115927     18.11             5.70      Cardiac signal from image data resampled and saved - pass 1
  20240326T115927     18.11             0.00      Phase waveform generated - pass 1
  20240326T115927     18.15             0.04      Slice phases determined for all timepoints - pass 1
  20240326T115927     18.15             0.00      Output arrays allocated - pass 1
  20240326T115927     18.15             0.00      Phase projection to image started - pass 1
  20240326T115941     32.12            13.97      Phase projection to image completed - pass 1
  20240326T115941     32.12             0.00      Phase projected data saved - pass 1
  20240326T115941     32.92             0.79      Vessel masked phase projected data saved - pass 1
  20240326T115941     32.96             0.04      Masks saved - pass 1
  20240326T115941     32.98             0.02      Cardiac signal generated from image data - pass 2
  20240326T115942     33.00             0.02      Cardiac signal from image data analyzed - pass 2
  20240326T115947     38.84             5.84      Cardiac signal from image data resampled and saved - pass 2
  20240326T115947     38.94             0.10      Phase waveform generated - pass 2
  20240326T115947     38.98             0.04      Slice phases determined for all timepoints - pass 2
  20240326T115948     38.99             0.01      Output arrays allocated - pass 2
  20240326T115948     38.99             0.00      Phase projection to image started - pass 2
  20240326T120000     51.88            12.90      Phase projection to image completed - pass 2
  20240326T120006     57.37             5.48      Phase projected data saved - pass 2
  20240326T120007     58.15             0.78      Vessel masked phase projected data saved - pass 2
  20240326T120007     58.28             0.13      Masks saved - pass 2
  20240326T120007     58.41             0.13      Done
  [user@cn3335 ~]$ exit
  [user@biowulf ~]$