Paravision 6

All mice were anesthetized by 1–3% isoflurane in 100% O2. The heads of the mice were placed with the animal's incisors secured over a bite bar and ophthalmic ointment was applied to the eyes. Animals were imaged in vivo with a T2-weighted Turbo-RARE (Rapid Acquisition with Relaxation Enhancement) and an isotropic T1-weighted FLASH sequence in a 7 T small animal MRI-scanner (BioSpec 70/30, gradient insert: BGA-12S, maximum gradient strength: 440 mT/m, Software interface: Paravision 6.01., Bruker BioSpin GmbH, Ettlingen, Germany) which was equipped with a 1H cryogenic, two elements, transmit/receive coil array. Animal welfare was ensured by employing a water driven warming mat as well as constant respiration and core body temperature monitoring.

MRI measurements were performed seven and 35 days after surgery with an 11.7T BioSpec Avance III small animal MR system (Bruker BioSpin, Ettlingen, Germany) operating on Paravision 6.0.1. software (Bruker, Karlsruhe, Germany) under full isoflurane anaesthesia (3.5% for induction and 1.8% for maintenance; in a 2:1 (medical air:oxygen) mixture). Body temperature was monitored with a rectal probe, and maintained at 37 °C using hot air flow. A pneumatic cushion respiratory monitoring system (Small Animal Instruments Inc., Stony Brook, New York, NY, USA) was used to measure the respiration rate of the mouse. Mice with scans that showed motion and/or echo planar imaging artifacts were excluded from MRI analysis.

Each animal was anesthetized with halothane (3–4% induction, 1.5–2% maintenance) in oxygen (0.4 L min⁻¹) and nitrogen (0.6 L min⁻¹). After anesthesia, each rat was placed on the fixation system in prone position. The experiments were performed on a small animal MRI system (Bruker BioSpec 7T/20 USR, Germany). The sequence protocol included T2-weighted, 256 × 256 matrix, slice thickness 1 mm, intersection gap 1 mm, echo time (TE)/repetition time (TR) 27/3000 ms, RARE factor 16, and flip angle 90°. T2-weighted images were acquired in the sagittal and axial planes by the ParaVision 6.0.1 (Bruker BioSpec, Germany). The area of the lesioned spinal cord containing hyperintense signal was first manually traced by a blinded observer. A computer-aided software (FireVoxel; CAI2R, New York University, NY) was used for axial images to assess and compare the evolution of hyperintense signal and lesion volume obtained by adding the individual slice areas and multiplying by 1.0 mm slice plus gap thickness. For quantitative analysis, the results were calculated by the intensity ratio for the signal of spinal cord lesion to normal cord far from injury area.

DW MRI data were processed via vendor specific software (Image Display and Processing tool, Bruker Paravision 6.0.1). ADC-maps were calculated on a pixel by pixel basis from DW MRI data using a least square mono-exponential fitting [28 (link)]. To compute the mean ADC of the solid tumor tissue, hand drawn ROIs were placed in each transaxial tumor slice following the outer surface of tumor tissue. Afterwards these ROIs were used for creating VOIs.