Magnetom verio 3

MRI experiments were carried out on a 3.0 Tesla MR scanner (Siemens, MAGNETOM Verio 3.0; Munich, Germany) with a wrist coil at 4 wpi. Under anaesthesia, sagittal T2-weighted turbo spin-echo images (T2WI) of thoracic vertebra were acquired from the animals with the following parameters: repetition time (TR) = 3610 ms; echo time (TE) = 74 ms; slice thickness = 1.0 mm; field of view (FOV) = 120 mm×120 mm; average = 3.

MRI of the brain and spine were acquired on a Siemens MAGNETOM Verio 3.0 Tesla scanner. Pre, post, dynamic contrast enhanced, dynamic susceptibility contrast, gadolinium T1-weighted, diffusion and T2-weighted sequences were acquired. Tumor foci were measured on axial T1 multi-planar reconstruction (MPR)-weighted images obtained after the administration of MultiHance (gadobenate dimeglumine). Response assessment was recorded using the modified RANO criteria for GBM. Imaging with ¹⁸F-fluorodeoxyglucose was performed using a GE Discovery DST HP60 PET-CT scanner (70 cm axial field of view, slice thickness 3.75 mm). Maximal standardized uptake values were obtained utilizing Vital Images Vitrea version 6.7.2 software. For the calculation of contrast-enhancing tumor volumes, T2-weighted, T2-weighted Fluid Attenuated Inversion Recovery, T1-weighted pre- and post- contrast images were coregistered and resampled to 1 mm × 1 mm × 3 mm voxel sizes using BraTumIA software^{50 (link)}. The registered, non-skull-stripped images were then imported into ITK-SNAP (v3.8.0) for segmentation^{51 (link)}. Trained readers generated initial masks of the tumor volumes with final review and volume selection by a radiologist with over 10 years of experience in neuroradiology.

The pre-operative MRI protocol (Siemens-Magnetom-Verio-3.0) included: axial-three-dimensional-(3D)-FLAIR; post-Gd-three-dimensional-T1-weighted; DWI-ADC diffusion-weighted imaging. Patients underwent post-operative-MR (volumetric-FLAIR and post-GdT1-weighted) both within 48 h and 2 months to estimate EOR [10 (link),15 (link),21 (link)]. An immediate post-operative-DWI was performed to evaluate ischemia [10 (link),12 (link)].

Magnetic resonance imaging (MRI) data were collected on a Siemens Magnetom Verio 3 Tesla scanner. A structural image was acquired using an MP2RAGE sequence (TR = 5000 ms, TE = 2.92 ms, TI1 = 700 ms, TI2 = 2500 ms, flip angle 1 = 4°, flip angle 2 = 5°, voxel size = 1.0 mm isotropic, duration = 8.22 min; Marques et al. 2010 (link)). Four resting-state functional MRI scans were acquired using a multiband EPI sequence (TR = 1400 ms, TE = 39.4 ms, flip angle = 69°, multiband acceleration factor = 4, voxel size = 2.3 mm isotropic, 64 slices, 657 volumes, duration = 15.30 min; Feinberg et al. 2010 (link); Moeller et al. 2010 (link)). Sequences were identical across runs with the exception of alternating phase encoding and slice orientation (AC–PC axis and aligned to orbitofrontal cortex) to vary the spatial distribution of signal loss across runs. During resting-state scans, participants were instructed to fixate on a crosshair. Field maps (TR = 680 ms, TE1 = 5.19 ms, TE2 = 7.65 ms, flip angle = 60°, voxel size = 2.3 mm isotropic, 64 slices) were obtained separately for each resting-state run to correct for magnetic field inhomogeneities.

MRI acquisition was performed using a Magnetom Verio 3 T scanner (Siemens, Erlangen, Germany). Table 1 presents acquisition parameters for MR sequences including T1-weighted magnetization-prepared rapid gradient-echo (MPRAGE), T2-weighted fluid-attenuated inversion recovery (FLAIR) and diffusion-weighted images along with a field map to aid correction of susceptibility distortions. All images were reviewed for neuroanatomical defects by qualified radiologists, who reported nil abnormal findings.Table 1

Magnetic resonance imaging (MRI) parameters

Parameter	T1-weightedMPRAGE	T2-weightedFLAIR	Diffusion-weightedImages	Field map
Scan timing
Echo time (TE, ms)	2.93	82	130	5.19 / 7.65
Repetition time (TR, ms)	2300	6000	8900	400
Inversion time (TI, ms)	900	2070	–	–
Flip angle (°)	9	125	90	60
Bandwidth (BW, Hz/pixel)	241	200	992	260
Echo train length (ETL)	1	24	1	1
b-values	–	–	0, 3000	–
Acquisition timing
Frequency (number of pixels)	240	320	120	64
Phase (number of pixels)	256	320	120	64
Phase field of view (FOV, %)	0.94	1.00	1.00	100
Gradient directions	–	–	64	–
b-zeros	–	–	1	–
Scanning range
FOV (mm)	253 × 270	250 × 250	240 × 240	192 × 192
Spacing (mm)	1.05	0.78	3	3.75
Slice thickness (mm)	1.2	2.5	2	3
Slices	192	60	50	36

MPRAGE magnetization-prepared rapid gradient-echo, FLAIR fluid-attenuated inversion recovery

Brain MRI scans were conducted on a MAGNETOM Verio 3-tesla scanner (Siemens Medical Systems, AG, Erlangen, Germany) with volumetric values derived from T1-weighted images via FreeSurfer, version 6 (16 (link)).
Volumetric segmentation was performed on the MPRAGE sequence using the Freesurfer, version 6.0, image analysis suite (http://surfer.nmr.mgh.harvard.edu/). The procedures for measuring cortical thickness have been validated against histological analysis and manual measurements. Freesurfer morphometric procedures have demonstrated good test–retest reliability across scanner manufacturers and across field strengths.
Conventional sagittal 3D magnetization-prepared rapid acquisition with gradient echo (MPRAGE) T1 [voxel size = 1 × 1 × 1.2 mm; flip angle/repetition time (TR)/echo time (TE)/inversion time (TI) = 9/2300/2.98/900 ms; scan time = 9:14] and axial turbo spin-echo T2 (voxel size = 0.8 × 0.8 × 4 mm; TR/TE =5,000/84 ms; 38 slices; scan time = 0:57).