Clinscan system

After adeno-Cre instillation, tumors were monitored via MRI and when tumor burden was measurable, mice were placed on one of four arms of a treatment regimen. Animals were anaesthetized via inhalation of isoflurane and kept warm on heated waterbed, vitals were monitored via cardiac and respiratory cycle (SA instruments), and recorded every 10 minutes while the animal was under anesthesia. The SA instruments pneumatic respiratory monitor was used to remove breathing artifacts by gating on the respiratory cycle. The Bruker ClinScan system used to scan the animals had 12 cm of actively shielded gradients, maximum strength 630 mT/m, and a slew rate of 6,300 T/m/second. This instrument is a 7T system with 2 × 2 array coil and 2D gradient echoT1-weighted sequences. The parameters used for imaging are as follows: 18 slices, TR = 170 ms, TE = 2.4 ms, α = 38°, Navg = 3, FOV 26 × 26 mm², 1 mm thickness, matrix size 256 × 256, for a voxel size of 0.102 × 0.102 × 1.0 mm. In 2021, the system was upgraded to a Bruker Biospec system. For this upgraded machine, the Bruker IntraGate software was used to remove respiratory and cardiac motion with parameters: 18 slices, TR = 8.96ms ms, TE = 3.4 ms, α = 10°, oversampling = 28, FOV 26 × 26 mm2, 1 mm thickness, matrix size 192 × 192, 10 minutes. Models were then built on Slicer three-dimensional (3D) software to calculate tumor volume.

All mouse imaging was performed on a 7 T Bruker ClinScan system (Bruker, Ettlingen, Germany) equipped with a 4-element phased array cardiac coil. Short-axis images (basal, mid-ventricular, apical) and long-axis images (two and four-chamber) were acquired with 13–20 frames per cardiac cycle. In-plane displacements were encoded for each image. Acquisition parameters were: TR = 7.4 ms, TE = 1.0 ms, Acquisition Matrix = 128 × 128, Pixel Spacing = 0.25 mm, Slice Thickness = 1 mm, Flip Angle = 20°, 36 inter-leaved spirals, displacement encoding frequency (k_e) =1.0 cycles/mm.
Human subject imaging was performed on either a 3 T Siemens Tim Trio or 1.5 T Siemens Avanto system (Siemens Healthcare, Erlangen, Germany) with a 6-element phased array cardiac coil and a 24-element spine coil. Short-axis images (basal, mid-ventricular, apical) and long-axis images (two and four-chamber) were acquired with 17–28 frames per cardiac cycle. In-plane displacements were encoded for each image. Acquisition parameters were: TR = 17 ms, TE = 1.1 ms, Acquisition Matrix = 128 × 128, Pixel Spacing = 2.6 – 2.8 mm, Slice Thickness = 8 mm, Flip Angle = 20°, 6 inter-leaved spirals, k_e = 0.1 cycles/mm.