seeVR is an open-source MATLAB toolbox for analyzing cerebrovascular imaging data — especially CVR (cerebrovascular reactivity) based on BOLD/fMRI. It ships with ready-to-use functions for CVR mapping, lag analysis, HRF modeling, denoising, spectral metrics (e.g., fALFF), plus a 3-D/4-D viewer (seeVieweR) for high-quality visualization and export.
- Purpose-built for CVR & hemodynamics: pipelines and helpers aimed at hypercapnia/breath-hold/resting-state use cases.
- From data to maps: CVR, lag-corrected CVR, HRF/dispersion/onset metrics, spectral features (fALFF), plus utilities (regression, filtering, masks).
- Batteries included: seeVieweR 3-D/4-D viewer for overlays, masks, erosion, slice controls, and movie/snapshot export.
- Published & used by the community: tutorials and references available (ISMRM, MR-Hub, lab tutorials).
- CVR mapping: basic/GLM CVR indices, lag-aware CVR. (
basicCVR,gasslessCVRx,lagCVR)
- HRF modeling: convolve and fit (onset/dispersion) via HRF/EXP kernels. (
fitTau,convHRF,fitHRF)
- Aligment of physiological traces: manual or automatic. (
autoAlign,trAlign) - Spectral metrics: fALFF and frequency spectra. (
fALFF,freqSpec) - Preprocess & cleanup: nuisance regression, scrubbing, band-pass, normalization, timeseries utilities. (
filtRegressor,scrubData,genGS,remLV,smthData,denoiseData,grabTimeseries,normTimeseries,chopTimeseries,demeanData,trAlign) - I/O & helpers: NIfTI handling (via built-in functions or Jimmy Shen’s toolbox), plotting, registration helpers, and more.
- 3-D/4-D volume viewer with overlays, color/alpha control, slice masks (X/Y/Z), vessel erosion (skeleton protection), colormap flipping, lighting/denoising toggles, background, and export (PNG/SVG/GIF/MP4).
- Walk-throughs for CO₂ CVR and breath-hold/resting-state CVR, with template scripts.
Tutorials and test data available at the seeVR toolbox website
main_functions/,functions/,helper/,plotting/,read_write/,registration/— analysis code, utilities & helpers.seeVieweR/— Visualization tool (3-D/4-D).gas_import/,resources/— domain-specific helpers/resources.
git clone https://github.com/abhogal-lab/seeVR.git