Introduction:

Distinguishing cortical layers and investigating depth-dependent BOLD [1] responses in isotropic submillimeter-resolution fMRI [2] require the use of a high-contrast distortion- and resolution-matched (DRM) anatomy. Based on our earlier work of DRM anatomical MR image acquisitions for T1w-Like image reconstruction [3,4], we present here the results of isotropic submillimeter-resolution fMRI on a T1w-Like whole-brain anatomical image reconstructed from the image inversion of DRM T1-maps. These T1-maps are computed from slice varying multi-shot inversion recovery-prepared echo-planar imaging (msIR-EPI) volumes [5, 6]. The same pulse sequence was used for acquiring both functional and DRM anatomical images with aligned slice acquisitions except differing in parameters unrelated to distortions. The reconstructed T1w-Like anatomy in the native EPI space offers high alignment necessary for activity localization providing benefits for studying voxel-wise dynamics in isotropic submillimeter-resolution fMRI. Moreover, the proposed T1w-Like anatomy allows the generation of cortical surface for investigating depth-dependent responses [7].

Materials & Methods:

An adult human brain was scanned using the BISEPI sequence [2] on a Siemens MAGNETOM 7T scanner with a 32-channel phased-array head coil to obtain 144 fMRI volumes at a spatial resolution of voxel-wise 0.7 mm isotropic. The functional scan (#Segments = 3, GRAPPA = 2, #Shots in block = 24, TR/TE/FA = 1000 ms /22.2 ms / 50°, #Slices = 15, PF = 6/8) covering the region of interest in primary motor cortex was acquired in a bilateral finger tapping block-design task 12s (ON) / 12s (OFF). Functional scan was followed by five slice-shifted anatomical volumes at a spatial resolution of voxel-wise 0.7 mm isotropic using 2D msIR-EPI (#Segments = 6, TR/TE/FA = 3000 ms /22.2 ms/ 90°, Slices/Averages = 35x5/2, Slice thickness = 0.7 mm, Spacing = 3.5 mm, PF = 6/8) with variable inversion recovery for each slice generated by an IR-sweep with varying inversion time (TI) across slices (TI=100-2400ms) [6]. The obtained anatomical volumes were used to generate T1-maps after T1-fitting and combined and processed in Matlab to generate whole-brain T1w-Like DRM anatomy based on image inversion [4]. The obtained native EPI space T1w-Like anatomy was post-processed in BrainVoyager for generating cortical surface after AC-PC transformation. Mid-GM surface was generated and the functional data at four distinct depths moving from GM-WM interface to GM-pial boundary were sampled and overlaid on this mid-GM surface. fMRI pre-statistics processing includes mean intensity correction, motion correction, and high-pass filtering with GLM-Fourier 2 sines/cosines and Gaussian FWHM of 2 data points, with no spatial smoothing. The generalized linear model analysis was applied with stimulation ON/OFF as a binary regression variable in BrainVoyager 21.2.

Results and Discussion:

Figure 1 shows fMRI BOLD activity overlaid on the obtained T1w-Like DRM anatomy based on image inversion [4]. As shown here, the fMRI BOLD activity at 0.7 mm isotropic resolution follows the ribbon of the grey matter structures on the reconstructed T1w-Like DRM whole-brain anatomy. Figure 2 shows the mid-GM cortical surface generated from this anatomy where fMRI BOLD activity is sampled at distinct cortical depths moving from the GM-WM interface (left-most) to the GM-pial boundary (right-most). Figure 3 shows overlaid fMRI BOLD activity as the multiple-selection of all depth maps on the mid-GM cortical surface.

Conclusion:

DRM T1w-Like anatomy in the native EPI space [3, 4] alleviates the problem of distortion mismatch that exists between function and T1w anatomy. Moreover, it improves the accuracy of activity localization and interpretation of the results in submillimeter-resolution fMRI studies. In this study, we reconstructed T1w-Like whole-brain DRM anatomical slices from the image inversion of T1-maps computed from slice varying 2D msIR-EPI [5, 6] acquired at 0.7 mm isotropic resolution. The reconstructed T1w-Like DRM anatomy demonstrates a strong alignment with the acquired functional data, necessary for studying voxel-wise dynamics in submillimeter-resolution fMRI. The proposed T1w-Like whole-brain anatomy allows the generation of a cortical surface, useful for investigating layer-specific functional responses in a region of interest.

Acknowledgements

This study was supported in part by Japan Society for the Promotion of Science (JSPS) Grants-in-Aid for Scientific Research “KAKENHI” (Grant Numbers JP26282223 and JP26350471 and JP19K08244).

References

[1] Ogawa S, Lee TM, Kay AR, Tank DW. Brain magnetic resonance imaging with contrast dependent on blood oxygenation. Proc Natl Acad Sci USA. 1990;87(24):9868-9872. [2] Liu G, Shah A, Ueguchi T. Block-Interleaved segmented EPI for voxel-wise high-resolution fMRI studies at 7T. Proceedings of the International Society for Magnetic Resonance in Medicine Joint Annual Meeting ISMRM-ESMRMB. 2018;5450. [3] Shah A, Ueguchi T, Liu G. Distortion-Matched Anatomical Imaging using Inversion Recovery-Prepared EPI for high-resolution fMRI. 24th Annual Meeting of the Organization for Human Brain Mapping. 2018;1727. [4] Shah A, Liu G, Ueguchi T. EPI based distortion- and resolution-matched T1-Like anatomy for submillimeter-resolution fMRI at 7T. 25th Annual Meeting of the Organization for Human Brain Mapping. 2019;2591. [5] Turner R, Panchuelo RS, Mougin O, Francis S. Multi-shot inversion recovery EPI with SMS excitation for high spatial resolution T1-mapping. 25th Annual Meeting of the Organization for Human Brain Mapping. 2019;2627. [6] Panchuelo RS, Turner R, Mougin O, Francis S. A 2D multi-shot inversion recovery EPI (MS-IR-EPI) sequence for high spatial resolution T1-mapping at 7T. Proceedings of the International Society for Magnetic Resonance in Medicine. 2018;60. [7] Shah A, Liu G, Ueguchi T. Investigating Depth-Dependent Activity in Submillimeter-Resolution fMRI at 7T with Native- Space Transformed T1w MPRAGE Anatomy. ICMRI. 2019;SS03-08.