Sensory and optogenetically driven single-vessel fMRI

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Abstract

Magnetic resonance imaging (MRI) sensitivity approaches vessel specificity. We developed a single-vessel functional MRI (fMRI) method to image the contribution of vascular components to blood oxygenation level–dependent (BOLD) and cerebral blood volume (CBV) fMRI signal. We mapped individual vessels penetrating the rat somatosensory cortex with 100-ms temporal resolution by MRI with sensory or optogenetic stimulation. The BOLD signal originated primarily from venules, and the CBV signal from arterioles. The single-vessel fMRI method and its combination with optogenetics provide a platform for mapping the hemodynamic signal through the neurovascular network with specificity at the level of individual arterioles and venules.

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Figure 1: Single-vessel fMRI overlaps with the A-V map.
Figure 2: Optogenetically induced fMRI signal from single vessels penetrating the barrel cortex.
Figure 3: Temporal features of sensory and optogenetically driven BOLD and CBV fMRI signals from individual arterioles and venules.

Change history

  • 29 February 2016

    In the version of this article initially published online, color labels in Figure 1f were erroneously switched. The error has been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

This research was supported by the Intramural Research Program of the US National Institutes of Health, the US National Institute of Neurological Disorders and Stroke and internal funding from the Max Planck Society. We thank H. Schulz, S. Fischer, K. Sharer and N. Bouraoud for technical support and A. Bonci for help with the optogenetic setup.

Author information

Affiliations

Authors

Contributions

X.Y. and A.P.K. initiated the work, developed the method and wrote the paper. A.C.S. and S.J.D. helped setup the k-space reconstruction. H.M. and S.J.D. designed the radiofrequency coil. X.Y. performed MRI experiments at 11.7 T and 14 T. Y.H. and M.W. helped with 14-T MRI data acquisition and analysis.

Corresponding authors

Correspondence to Xin Yu or Alan P Koretsky.

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Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 BOLD and CBV functional maps showing EPI versus line-scanning FLASH fMRI.

A. Colored BOLD and CBV functional maps are shown in the highlighted window (green frame) of the raw EPI images (representative of 3 rats). B. Colored BOLD and CBV functional maps are shown in the highlighted window (green frame) of the raw FLASH images (representative of 5 rats). C and D. The BOLD (red) and CBV (blue) fMRI time courses were averaged from the sparsely distributed voxels with β values at thresholds (BOLD, β ≥ 5; CBV, β ≤ -5, mean±SD).

Supplementary Figure 2 The line-scanning–based FLASH fMRI method.

A. The overall view on the k-space acquisition of the FLASH-fMRI method. At each trial of the block-design experiment (red line), one k space line was acquired for each image. The k space for each image was filled with one line at each trial. Experimental trials were repeated for the number of phase-encoding steps (N=32/64). B. The k space map was reconstructed to produce the 2D image, which was located at the deep layer cortex (1.0mm to the cortical surface) covering the primary somatosensory cortex.

Supplementary Figure 3 Time-lapsed BOLD fMRI images with line-scanning fMRI.

The grey-scale BOLD functional maps are shown as the function of time at every 100ms from 0s to 2s following the stimulus onset. The raw image is shown in the upper left corner.

Supplementary Figure 4 Time-lapsed CBV fMRI images with line-scanning fMRI.

The grey-scale CBV functional maps are shown as the function of time at every 100ms from 0s to 2s following the stimulus onset. The raw image (after iron injection) is shown in the upper left corner.

Supplementary Figure 5 Localization of BOLD and CBV fMRI voxels.

A. BOLD and CBV functional maps from the 2D anatomical image (T2*w) in gray-scale (middle) and color-scale (right; BOLD, red; CBV, green, inversed). B. The BOLD and CBV functional color-maps overlapped with the sparsely distributed active voxels in the same 2D slice (left). Both enlarged functional maps were overlapped on the anatomical T2*W images (right).

Supplementary Figure 6 The detection of individual penetrating arterioles and venules in the deep layer cortex.

A. The representative A-V map from 6 rats. The individual venules are shown as dark voxels (blue crosses). The individual arterioles are shown as bright voxels (red circles). B. The signal intensity of the venule (23) and arteriole (25) voxels was plotted as the function of different TEs from 2.5ms to 15ms (one representative rat from A. C. The averaged signal intensity of all venule and arteriole voxels was plotted as the function of different TEs (n=6, rats, mean±SEM).

Supplementary Figure 7 The light-driven local field potential (LFP) by optogenetics.

A. The LFP trace by optical stimulation (upper panel: 1ms light pulse, 3Hz, 10mw; lower panel, 20ms light pulse, 1Hz, 10mw). B. The averaged LFP driven by 1ms light pulse at different power (0, 0.3, 1.2, 5, 10, 20 mw) and by electrical stimulation of the whisker barrel (2.0mA, 3Hz, 0.3ms, red dotted line). C. The averaged LFP driven by light pulse at different duration (0.3, 1, 5, and 20ms; 3Hz, 10mw).

Supplementary Figure 8 Light-driven BOLD and CBV fMRI signal acquired by EPI methods.

A. The T2*-weighted images with the fiber optic inserted to target the barrel cortex in two consecutive slices. B. The colored BOLD fMRI maps show the most active voxels close to the fiber tip (upper panel) with anatomical image overlay (lower panel). C. The colored CBV fMRI maps show the most active voxels close to the fiber tip after iron oxide particle injection (upper panel) with anatomical image overlay (lower panel). D. The voxel-wise BOLD fMRI time courses (2s on/ 20s off, 8 epochs) plotted in a 3x3 matrix (the voxel position is shown in the colored BOLD-fMRI map, left). E. The voxel-wise CBV fMRI time courses (2s on/ 20s off, 8 epochs) plotted in a 3x3 matrix (the voxel position is shown in the colored CBV-fMRI map, left).

Supplementary Figure 9 The BOLD and CBV fMRI signal from individual arterioles and venules under 14.1 T.

A. A representative A-V map from 4 rats. The individual arteriole and venule voxels were detected with different signal intensity (venule voxels, blue; arteriole voxels, red). B. The BOLD fMRI time courses (raw data and fitting curves) from individual venule voxels(upper panel) and the CBV fMRI time courses (raw data and fitting curves) from individual arteriole voxels (lower panel). C. The fMRI onset time (t0) maps (left panel) and time-to-peak (ttp) maps (right panel) of a representative rat. D. 3d plots of the onset-time (t0), time-to-peak (ttp), and full-width-of-half-maximum (FWHM) of fMRI signal from individual arteriole (red diamonds, 39, r2>0.4) and venule (blue circles, 63, r2>0.5) voxels from 4 rats. E. Distribution of number of venule (blue) and arteriole (red) voxels with different t0, ttp and FWHM.

Supplementary Figure 10 The BOLD fMRI signal from individual arterioles and venules.

A. The BOLD fMRI time courses (raw data and fitting curves) of two representative rats from total 5 rats (venules, upper panel; arterioles, lower panel). B. 3d plot of the onset-time (t0), time-to-peak (ttp), and full-width-of-half-maximum (FWHM) of fMRI signal from individual arteriole (red circles, 41, r2>0.4) and venule (blue circles, 71, r2>0.5) voxels from 5 rats. C. Distribution of the number of venule (blue) and arteriole (red) voxels with different t0, ttp and FWHM.

Supplementary Figure 11 The CBV fMRI signal from individual arterioles and venules.

A. The CBV fMRI time courses (raw data and fitting curves) of two representative rats from total five rats (arterioles, left; venules, middle, r2>0.2, right, r2 ≤0.2). B. 3d plot of the onset-time (t0), time-to-peak (ttp), and full-width-of-half-maximum (FWHM) of fMRI signal from individual arteriole (red diamonds, 59, r2>0.4) and venule (blue circles, 35, r2>0.2) voxels from 5 rats. C. Distribution of number of venule (blue) and arteriole (red) voxels with different t0, ttp and FWHM.

Supplementary Figure 12 The spatial and temporal characterization of the outlier vessel hemodynamic signal.

A. The A-V maps of two representative rats (red arrows for venule outliers, yellow arrows for arteriole outliers). B. The onset-time (t0) based A-V maps showed the BOLD t0 values of different venules and CBV t0 values of different arterioles of two representative rats (the outlier vessels are marked in numerical numbers). C. The time course of the hemodynamic signal from the outlier vessel voxels and their fitting curves. D. The scatter plot of the venule BOLD (left, dots, green line: 0.7s) and arteriole CBV (right, diamonds, green line: 0.9s) t0 values with the fitting r2 values (rat #1, yellow borders, rat #2, blue borders).

Supplementary Figure 13 Supplementary Figure 13 Group analysis of BOLD and CBV fMRI signals from individual vessels.

A. The averaged onset time(t0), time-to-peak (ttp), and full-width-of-half-maximum (FWHM) from arteriole CBV signal (red) and venule BOLD signal (blue) acquired from 11.7T (top panel; n=5; * p=0.002; & p=0.00001, # p=0.002), 14.1T (middle panel, n=4; * p=0.002; &, p=0.0006; # p=0.01), and driven by optogenetic method under 14.1T (bottom panel; n=4; * p=0.01; & p=0.002, # p=0.04. B. The averaged r2 values of all individual vessels were plotted for each rat of two experiments (11.7T: green, n=5, 14.1T: yellow, n=4; optogenetics: dark, n=4; error bar is ±SEM). Students’ t-test was used for statistical analysis. Source data

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–13, Supplementary Table 1 and Supplementary Note 1 (PDF 3308 kb)

The BOLD and CBV fMRI signal changes with FLASH-fMRI.

The left panel shows the BOLD fMRI signal changes as the function of time every 100ms after the stimulus onset. The right panel shows the CBV fMRI signal changes as the function of time every 100ms after the stimulus onset. The grey scale of the image indicates the level of the fMRI signal beta values (β). (AVI 5432 kb)

The single-vessel BOLD fMRI signal changes with line-scanning fMRI under 11.7 T.

The single vessel BOLD fMRI signal changes as the function of time every 100ms after the stimulus onset. The left panel demonstrates the location of the 2D slice perpendicular to the penetrating vessels (1.0-1.5mm depth covering the forepaw somatosensory cortex, FP-S1). The right panel shows the A-V map (in plane 75×75 μm) as the background (dark voxels as venules, bright voxels as arterioles). The movie shows the most active voxels (red color, 150×150 μm) were primarily located at the underlying venules (dark dots). (AVI 848 kb)

The single-vessel CBV fMRI signal changes with line-scanning fMRI under 11.7 T.

The single vessel CBV fMRI signal changes as the function of time every 100ms after the stimulus onset. The left panel demonstrates the location of the 2D slice perpendicular to the penetrating vessels (1.0-1.5mm depth covering the forepaw somatosensory cortex, FP-S1). The right panel shows the A-V map (in plane 75×75 μm) as the background (dark voxels as venules, bright voxels as arterioles). The movie shows the most active voxels (blue color, 150x150 μm) were primarily located at the underlying arterioles (bright dots). (AVI 1013 kb)

The BOLD fMRI signal changes with voxel-wise time courses under 11.7 T.

The voxel-wise BOLD fMRI signal changes were demonstrated from 5x5 voxel matrix covering one individual venule (the dark voxel in the black square, middle panel, in plane: 75×75 μm). The red curser moves in the center voxel (100ms temporal resolution) corresponding to the color-coded BOLD functional movie (right panel). (AVI 6969 kb)

The CBV fMRI signal changes with voxel-wise time courses under 11.7 T.

The voxel-wise CBV fMRI signal changes were demonstrated from 5×5 voxel matrix covering one individual venule (the bright voxel in the black square, middle panel, in plane: 75×75 μm). The red curser moves in the center voxel (100ms temporal resolution) corresponding to the color-coded CBV functional movie (right panel). (AVI 6255 kb)

The single-vessel BOLD fMRI signal changes with line-scanning fMRI under 14 T.

The single vessel BOLD fMRI signal changes as the function of time every 100ms after the stimulus onset. The left panel demonstrates the location of the 2D slice perpendicular to the penetrating vessels (1.0-1.5mm depth covering the forepaw somatosensory cortex, FP-S1). The right panel shows the A-V map (in plane 50×50 μm) as the background (dark voxels as venules, bright voxels as arterioles). The movie shows the most active voxels (red color, 100×100 μm) were primarily located at the underlying venules (dark dots). (AVI 593 kb)

The single-vessel CBV fMRI signal changes with line-scanning fMRI under 14 T.

The single vessel CBV fMRI signal changes as the function of time every 100ms after the stimulus onset. The left panel demonstrates the location of the 2D slice perpendicular to the penetrating vessels (1.0-1.5mm depth covering the forepaw somatosensory cortex, FP-S1). The right panel shows the A-V map (in plane 50×50 μm) as the background (dark voxels as venules, bright voxels as arterioles). The movie shows the most active voxels (blue color, 100×100 μm) were primarily located at the underlying arterioles (bright dots). (AVI 763 kb)

The BOLD fMRI signal changes with voxel-wise time courses under 14 T.

The voxel-wise BOLD fMRI signal changes were demonstrated from 7×7 voxel matrix covering one individual venule (the dark voxel in the white square, middle panel, in plane: 50×50 μm). The red curser moves in the center voxel (100ms temporal resolution) corresponding to the color-coded BOLD functional movie (right panel). (AVI 2978 kb)

The CBV fMRI signal changes with voxel-wise time courses under 14 T.

The voxel-wise CBV fMRI signal changes were demonstrated from 7×7 voxel matrix covering one individual venule (the dark voxel in the white square, middle panel, in plane: 50×50 μm). The red curser moves in the center voxel (100ms temporal resolution) corresponding to the color-coded CBV functional movie (right panel). (AVI 6003 kb)

Voxel-based 3D plot of BOLD and CBV signal as a function of the signal intensity of A-V map voxels.

The 3d plot of the BOLD/CBV fMRI signal beta values from individual voxels with normalized signal intensity of the A-V maps (0-1). The data points from individual rats were color-coded differently. (AVI 2219 kb)

The light-driven single-vessel BOLD fMRI signal changes with optogenetics.

The light-driven single vessel BOLD fMRI signal changes as the function of time every 100ms after the stimulus onset. The left panel demonstrates the location of the 2D slice perpendicular to the penetrating vessels as well as the inserted fiber optic. The right panel shows the A-V map (in plane 50×50 μm) as the background (dark voxels as venules, bright voxels as arterioles). The movie shows the most active voxels (red color, 100×100 μm) were primarily located at the underlying venules (dark dots). (AVI 1213 kb)

The light-driven single-vessel CBV fMRI signal changes with optogenetics.

The light-driven single vessel CBV fMRI signal changes as the function of time every 100ms after the stimulus onset. The left panel demonstrates the location of the 2D slice perpendicular to the penetrating vessels as well as the inserted fiber optic. The right panel shows the A-V map (in plane 50×50 μm) as the background (dark voxels as venules, bright voxels as arterioles). The movie shows the most active voxels (blue color, 100×100 μm) were primarily located at the underlying arterioles (bright dots). (AVI 875 kb)

A 3D plot of temporal features of sensory-evoked single-vessel fMRI signal.

The onset-time (t0), time-to-peak (ttp), and full-width-of-half-maximum (FWHM) of fMRI signal from individual arteriole (red diamonds, n=59, r2>0.4) and venule (blue circles, 71, r2>0.5) voxels from 5 rats are shown in the 3d plot (n=5, rats). (AVI 3428 kb)

A 3D plot of temporal features of light-driven single-vessel fMRI signal.

The t0, ttp, and FWHM of light-driven fMRI signal from individual arteriole (red diamonds, n=33, r2>0.3) and venule (blue circles, 37, r2>0.35) voxels are shown in the 3d plot (n=4, rats). (AVI 880 kb)

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Yu, X., He, Y., Wang, M. et al. Sensory and optogenetically driven single-vessel fMRI. Nat Methods 13, 337–340 (2016). https://doi.org/10.1038/nmeth.3765

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