4.2. MR Methods

MR experiments were performed on a horizontal 11.7 T scanner (Bruker, Ettlingen, Germany) interfaced with Paravision 6.0.1. A 72-mm diameter ¹H quadrature volume coil (Bruker, Ettlingen, Germany) and a custom-built 10-mm diameter ¹⁷O surface coil were used. After automatic adjustments including ¹H RF calibration, global shimming and frequency adjustment, a fast low angle shot (FLASH) image was acquired for localization and shim volume preselection (TR/TE = 195/2.3 ms, field of view (FOV) = 4 cm × 4 cm, matrix size = 256 × 256). It was followed by a 3D B0 field map (TR/TE1/TE2 = 20/1.4/5.4 ms, FOV = 3 cm × 3 cm × 3 cm, matrix size = 64 × 64 × 64, NA = 8) with a signal-to-noise threshold of 10 for reconstruction. A ¹H PRESS scan (2048 points, 4.5 mm³) was used to evaluate the shim quality over the entire brain, before and after the shim calculation procedure was applied (MAPSHIM). The resulting full width at half maximum for ¹H ranged between 45 and 55 Hz in vivo. In the CTR and APP_swe/PS1_dE9 groups, RARE images were acquired (TR/TE = 3000/30 ms, RARE factor 8; FOV: 20 × 20 mm²; matrix size: 192 × 192; slice thickness: 0.5 mm) so that total brain and ventricles volumes were determined by automated segmentation using an in-house developed python library (https://sammba-mri.github.io/, accessed on 1 November 2018).

To maximize sensitivity and overcome the short T2* expected for ¹⁷O, in vivo ¹⁷O-MRI was acquired using a hard pulse ZTE approach. We first compared the 3D ZTE performance to that of a standard 3D CSI on natural abundance water phantom and in vivo. For both sequences, RF pulse (5-μs broad pulse, 100 W) and TR (1.8 ms) were kept identical. CSI acquisitions: For 3D CSI, echo time was set to TE = 0.3 ms, the minimum achievable TE value in our settings. The field of view was 24 × 24 × 24 mm³, the matrix size was 16 × 16 × 16, the number of complex points was 128 with a dwell time of 8.4 µs, and the number of averages was 3. Successive CSI blocks were acquired with 4 averages in 24.8 s each, and repeated 40 times. CSI post-processing: 3D complex data were exported to Matlab (The Mathworks Inc., Matlab, R2015b) and filtered with a Hamming window. FIDs were then zero filled to 256 points and a line broadening of 6000 Hz was applied to minimize the FID truncation artifact due to the short acquisition time (1 ms). After Fourier transform and spectral rephasing, voxelwise integration of the real part over 3720 Hz (9 points) was performed to generate CSI images. ZTE imaging acquisitions: ZTE cartesian matrix size was 32 × 32 × 32 for a field of view of 48 × 48 × 48 mm³, which was achieved with 3310 radial spokes, each acquired in 0.88 ms. Successive ZTE blocks were acquired with 4 averages in 24.8 s, and repeated 40 times. ZTE post-processing: Initial reconstruction was performed in Paravision 6.0.1 (Bruker, Ettlingen, Germany), including reggriding of the ZTE-MRI radial k-space onto a Cartesian k-space using a Kaiser-Bessel kernel, density compensation and apodization correction. Complex Cartesian data were exported to Matlab and filtered with a Hamming window. SNR calculation: Spatial response functions were calculated accounting for the Hamming filter for CSI, resulting in an effective volume V_eff = 2.84 mm³ for individual voxels, and for Hamming filter and T2* relaxation for ZTE acquisition, with a T2* of 1.3 ms in vivo (resulting in V_eff = 3.1 mm³), and 3.2 ms in free water (resulting in V_eff = 2.9 mm³), as estimated from unlocalized single pulse acquisitions. SNR was calculated for a pixel located close to the coil for ZTE and CSI images (averaged over the 40 repetitions) as:

where noise is a 6 × 6 pixels² region of interest outside of the object.

The temporal SNR was calculated as:

Inhalation experiments were conducted in CTR and APP_swe/PS1_dE9 mice with the same parameters as described above for SNR comparison except for TR = 1.3 ms (chosen to further maximize in vivo SNR), yielding an individual scan time of 18.2 s. A series of ZTE-MRI were continuously acquired before (5 min), during (200 s), and after (15 min) inhalation of 70%-enriched ¹⁷O₂ (Nukem Isotopes, GmbH, Alzenau, Germany). To that effect, the breathing circuit connected to the nose cone was transiently switched from ¹⁶O₂ delivery to a home-built gas delivery system (Figure 1e,f) that started to deliver 160 mL ¹⁷O-enriched O₂ over 200 s. The ¹⁷O₂ delivery system consisted of a 500 mL gas-tight acrylic syringe (Super Syringe Model S0500 TLL, PTFE Luer Lock, Hamilton France SARL, Villebon-sur-Yvette, France) and a modified infusion pump, which stepper motor was driven by an Arduino Uno R3 board (https://www.arduino.cc/en/main/software, accessed on 1 August 2019). A programmable tactile graphic user interface (µLCD-43PT, 4D Systems, Minchinbury, Australia) allowed prescribing the inhalation protocol parameters (volume, duration and start/stop control). Data were processed using the same steps as for the SNR comparison experiments, described in Section 4.2.1 above.