# Predicting the Aqueductal Cerebrospinal Fluid Pulse: A Statistical Approach
## 2 Materials and Methods
### Magnetic Resonance Acquisition and Processing  
Brain and neck MRI were acquired from all subjects, using a 1.5 Tesla scanner (Siemens Magnetom Avanto, Erlangen, Germany), equipped with an 8-channel head coil and a 4-channel neck coil. The acquisition protocol consisted of brain anatomical scan and neck vein morphological and hemodynamic sequences. First, brain and neck T1-weighted localizer, were acquired for the slice positioning of the subsequent sequences. Then, brain 2D dual-echo turbo spin echo allowed us to assess any anatomical abnormalities (TR = 2,650 ms, TE = 28/113 ms, echo train length = 5, flip angle = 150\({}^{\circ}\), 50 interleaved, 2.5-mm-thick axial slices with a matrix size = 256 \(\times\) 256, interpolated to 512 \(\times\) 512, FOV = 250 \(\times\) 250 mm). The neck vein morphology was assessed using a 2D time-of-flight (TOF) MR venography of the neck, with a saturation band positioned caudal to the 128 axial slices (in-plane resolution = 0.5 \(\times\) 0.5 mm\({}^{2}\), slice thickness = 3 mm, distance factor between subsequent slices = -20, FOV = 256 \(\times\) 192 mm\({}^{2}\), TR = 26 ms, TE = 7.2 ms, flip angle = 70\({}^{\circ}\)). Maximum intensity projection (MIP) was performed for the visualization of the veins with sagittal and coronal views. The MIPs allowed us to position the following sequence and to evaluate the morphology of the JIV and secondary drainage routes. Finally, arterial and venous flows through the main cervical vessels, CSF flow between the second and the third cervical vertebrae (C2/C3 level) (cCSF) and aCSF were assessed using three retrospective cardiac gated 2D PC MRI. The sequence parameters were respectively (blood/cCSF/aCSF): TR = 33.75/30.2/30.2 ms, TE = 5.11/7.6/7.6 ms, flip angle = 30\({}^{\circ}\)/10\({}^{\circ}\)/10\({}^{\circ}\), matrix size = 288 \(\times\) 384/256 \(\times\) 256/256 \(\times\) 256, pixel size = 0.67 \(\times\) 0.67/0.62 \(\times\) 0.62/0.45 \(\times\) 0.45 mm\({}^{2}\), slice thickness = 4/4.5/4.5 mm, and maximum encoding velocity Venc 60/15/15 cm/s. A finger pulse oximeter was used in order to reconstruct different time points in the cardiac cycle (CC), depending on the heart rate frequency. The slice of the PC sequences were positioned perpendicularly to the flow of interest: for the cervical blood flow, the sagittal neck localizer (Figure 1A) and the sagittal and coronal TOF MIP on the images (Figure 1B,C) were used for positioning the PC slice at the C2/C3 level perpendicularly to the IJVs (Figure 1A,B,C); for the cCSF flow the sagittal neck localizer was used for positioning perpendicularly to the spinal canal at C2/C3 level (Figure 1A); for the aCSF flow the sagittal T1-weighted brain localizer was used (Figure 1D) for positioning perpendicularly to the AoS. The flow data were processed with FlowQ software, an in-house program written in MATLAB (The Mathworks, Natick, MA, USA), with the methods described in [25] by a single trained examiner. Briefly, for every PC sequence, the processing consisted in manually drawing two kinds of regions of interest (ROIs) on the magnitude and phase images. The first one was placed in the structures of interest for their flow quantification, and the second one consisted of at least three ROIs in stationary structures near to the structure of interest, for the estimation and removal of the phase offset. The IJVs, vertebral veins (VVs), deep cervical veins (DCVs), internal carotid arteries, and vertebral arteries were segmented on the PC images with Venc = 60 cm/s (Figure 2A,B)). The contours were drawn in the first time point and copied for every time point in the CC, manually adjusting them if needed. When we visually detected a ROI that was affected by phase aliasing, pixel phase values were corrected with the algorithm described in a previous work [26].