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.
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 (https://www.mathworks.com/matlabcentral/fileexchange/58219-easy-bandpass-filter), MATLAB Central File Exchange.
- John D’Errico (2021). inpaint_nans (https://www.mathworks.com/matlabcentral/fileexchange/4551-inpaint_nans), MATLAB Central File Exchange.
- Daniel Baboiu (2021). Legendre polynomials (https://www.mathworks.com/matlabcentral/fileexchange/28008-legendre-polynomials), MATLAB Central File Exchange.
- Matt J (2021). Extract linearly independent subset of matrix columns (https://www.mathworks.com/matlabcentral/fileexchange/77437-extract-linearly-independent-subset-of-matrix-columns), MATLAB Central File Exchange.
- Benjamin Kraus (2021). nanconv (https://www.mathworks.com/matlabcentral/fileexchange/41961-nanconv), MATLAB Central File Exchange.
- John D’Errico (2021). SLM – Shape Language Modeling (https://www.mathworks.com/matlabcentral/fileexchange/24443-slm-shape-language-modeling), MATLAB Central File Exchange.
- Oliver Woodford (2021). SC – powerful image rendering (https://github.com/ojwoodford/sc), GitHub.
- Stephen Cobeldick (2021). ColorBrewer: Attractive and Distinctive Colormaps (https://github.com/DrosteEffect/BrewerMap), GitHub.
- Ander Biguri (2021). Perceptually uniform colormaps (https://www.mathworks.com/matlabcentral/fileexchange/51986-perceptually-uniform-colormaps), MATLAB Central File Exchange.
- Jimmy Shen (2021). Tools for NIfTI and ANALYZE image (https://www.mathworks.com/matlabcentral/fileexchange/8797-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.