Below is a list of publications that have provided inspiration for some of the functionality of the seeVR toolbox. Using seeVR, it should be possible to re-produce similar results using your own data. I’ve tried to give credit where it is due but if I missed something please contact me.

  1. A novel perspective to calibrate temporal delays in cerebrovascular reactivity using hypercapnic and hyperoxic respiratory challenges
    AA Champagne, AA Bhogal, NS Coverdale, CI Mark, DJ Cook, Neuroimage 187, 154-165
  2. Insights into cerebral tissue-specific response to respiratory challenges at 7T: evidence for combined blood flow and CO2-mediated effects
    AA Champagne, AA Bhogal, Frontiers in physiology 12, 18
  3. Physiological denoising of BOLD fMRI data using Regressor Interpolation at Progressive Time Delays (RIPTiDe) processing of concurrent fMRI and near-infrared spectroscopy (NIRS)
    BB Frederick, LD Nickerson, Y Tong, Neuroimage 60 (3), 1913-1923
  4. Time delay processing of hypercapnic fMRI allows quantitative parameterization of cerebrovascular reactivity and blood flow delays
    MJ Donahue, MK Strother, KP Lindsey, LM Hocke, Y Tong, BB Frederick, JCBFM 36 (10), 1767-1779
  5. An improved approach to detection of amplitude of low-frequency fluctuation (ALFF) for resting-state fMRI: fractional ALFF
    QH Zou, CZ Zhu, Y Yang, XN Zuo, XY Long, QJ Cao, YF Wang, YF Zang,Journal of neuroscience methods 172 (1), 137-141
  6. Cerebrovascular reactivity mapping using resting-state BOLD functional MRI in healthy adults and patients with Moyamoya disease
    P Liu, G Liu, MC Pinho, Z Lin, BP Thomas, M Rundle, DC Park, J Huang, …, Radiology 299 (2), 419-425
  7. Measuring cerebrovascular reactivity: the dynamic response to a step hypercapnic stimulus
    J Poublanc, AP Crawley, O Sobczyk, G Montandon, K Sam, DM Mandell, …, JCBFM 35 (11), 1746-1756
  8. Examining the regional and cerebral depth-dependent BOLD cerebrovascular reactivity response at 7 T
    AA Bhogal, MEP Philippens, JCW Siero, JA Fisher, ET Petersen, …, Neuroimage 114, 239-248
  9. A novel method of quantifying hemodynamic delays to improve hemodynamic response, and CVR estimates in CO2 challenge fMRI
    J Yao, HC Yang, JH Wang, Z Liang, TM Talavage, GG Tamer Jr, I Jang, …, JCBFM
  10. The resting-state fMRI arterial signal predicts differential blood transit time through the brain
    Y Tong, J Yao, JJ Chen, BB Frederick, JCBFM 39 (6), 1148-1160
  11. Using carpet plots to analyze transit times of low frequency oscillations in resting state fMRI
    B Fitzgerald, JF Yao, TM Talavage, LM Hocke, BB Frederick, Y Tong, Scientific reports 11 (1), 1-14

The seeVR also makes use of the following Matlab tools:

  • Wonsang You (2021). Easy Bandpass Filter (, MATLAB Central File Exchange. 
  • John D’Errico (2021). inpaint_nans (, MATLAB Central File Exchange. 
  • Daniel Baboiu (2021). Legendre polynomials (, MATLAB Central File Exchange. 
  • Matt J (2021). Extract linearly independent subset of matrix columns  (, MATLAB Central File Exchange. 
  • Benjamin Kraus (2021). nanconv (, MATLAB Central File Exchange. 
  • John D’Errico (2021). SLM – Shape Language Modeling (, MATLAB Central File Exchange. 
  • Oliver Woodford (2021). SC – powerful image rendering (, GitHub. 
  • Stephen Cobeldick (2021). ColorBrewer: Attractive and Distinctive Colormaps (, GitHub. 
  • Ander Biguri (2021). Perceptually uniform colormaps (, MATLAB Central File Exchange. 
  • Jimmy Shen (2021). Tools for NIfTI and ANALYZE image  (, MATLAB Central File Exchange. 

Finally I would like to acknowleadge the following colleagues for their suggestions, discussions and contributions: Allen A. Champagne, Mario Baez, Wouter Schellekens, Eva E. Grinsven, Jeroen Siero, Stefan Rademakers.

This work was partially funded by a VENI research grant awarded to Dr. Alex  Bhogal as part of Dutch Research Councils Talent Scheme (VENI.194.056: The Ischemic Fingerprint)