3D Cine Magnetic Resonance Imaging of Respiratory Motion in Mechanically Ventilated Mice and Rats

PEEP is the positive end-expiratory pressure applied by a mechanical ventilator at the end of a breath. We wanted to explore how the ventilator settings, particularly PEEP, affect the shape and movement of the thorax. We compare the results between mice and rats.

Currently, mainly ultrasound is used for visualizing ventilated animals. With accelerated motion-resolved cine imaging using 70 MRI in combination with an optimized anesthesia protocol, we successfully performed 3D imaging of mechanically ventilated mice and rats. So from the MR images, we segmented the lungs to study the movement and dimension of the thorax.

And we can, for example, assess if the thorax expands more in the craniocaudal or in the anterior-posterior direction. Our main focus lies on preventing diaphragm and lung injury in mechanically ventilated patients. In this project, we specifically study the parameter PEEP, but in the future, we also want to study other settings of the mechanical ventilator or use different types of genetically modified animal models.

To begin, calibrate the mechanical ventilator for use outside the MR room using the ventilator menu. Place the mechanical ventilator in the magnetic resonance or MR room. Pull the cables connected to the MR-compatible ventilator through the bore of the MR machine.

Next, connect the MR-compatible mechanical ventilator to the compressor and a source of oxygen flow. To prepare a positive end expiratory pressure or PEEP column, fill a 50-milliliter measuring column with water. Now, tape a respiratory cushion loosely to the MR cradle at the location where the thorax of the animal will be.

Position the anesthetized and tracheostomized animal supine in the MR cradle and place the appropriate magnetic resonance coil over it, ensuring the tracheotomy tube is properly positioned. Stop and disconnect the mechanical ventilator and anesthesia pump. Transport the animal to the MR room and reconnect it to the MR-compatible ventilator to start ventilating.

Insert the rectal thermometer probe. Place the sensor of the saturation and heart rate monitor on the hind limb of the animal. Connect the respiratory monitoring system to the respiratory cushion to ensure proper vitals.

Place the animal in the MR scanner with the coil centered over the thorax. And connect the radio frequency cables to the coil. Immerse the expiratory tubing six centimeters into the water column, administering six centimeters of water PEEP.

Acquire a scout with five images in coronal and axial orientations, ensuring that the full thorax is within the field of view. Then acquire the 2D scans at six centimeters of water PEEP. Obtain 3D scan after placing the field of view around the complete thorax to cover the 2D scans.

After completing all the required scans, remove the animal from the scanner. To begin, obtain 2D and 3D MRI scans of the animal under mechanical ventilation, while applying positive end-expiratory pressure or PEEP. Open the software and click Load MRD to load the raw files.

Enter the respiratory rate set on the MR-compatible mechanical ventilator into heart respiration filters, and set the width to 15. Press Filter to apply the settings, resulting in a gated navigator signal. Ensure that the red signal in the respiration navigator and respiration rate boxes follow the blue raw navigator signal.

Select Respiratory Movie in the Cine tab, set the number of frames to 12 and the number of dynamics to one. In the reco parameters tab, enable PCA level eight and ringing filter. After applying the settings, press Reconstruct to initiate the reconstruction.

Check the reconstructed images and export them with the export DCM feature. For image analysis, open and select the desired frame of the 2D image in the DICOM viewer. Using the measurement button in microdicom, measure the anterior-posterior and craniocaudal lung dimensions in the sagittal 2D cine, and the left-right dimension in the coronal-oriented 2D cine.

After repeating these measurements for all PEEP levels, load the cine into the 3D image analysis program, reorient image under the Tools tab, and fill in SPL as RAI code. Scroll through the dynamics at tools followed by layer inspector and select the end-expiratory frame. Then, using paintbrush mode, initialize segmentation by manually contouring the middle part of the lungs in two slices for every orientation.

Start the 3D segmentation using the active contour function in the main toolbar. Enable initialize with current segmentation and press Segment 3D after ensuring complete thorax coverage. Select thresholding as the pres segmentation mode.

Use only an upper threshold with the right-most threshold mode, and press Next. Start active contouring with the play button. Pause it as soon as the segmentation reaches the edges of the lungs.

After verifying the images, press Finish to finalize. Now, press update to visualize the 3D segmentation and rotate the 3D visualization to inspect. To save the segmentation as a nifty file, click Segmentation followed by Save Segmentation Image.

Export the segmentation as an STL mesh file with the export segmentation mesh option. After noting the lung volumes, register the images of other respiratory states to the end-expiratory dynamic using the appropriate script, and apply the computed transformations to the segmentation. The high-quality MRI scans allowed monitoring of basic physiological parameters during mechanical ventilation of the animals at different levels of PEEP.

The sagittal orientation scans demonstrated that PEEP caused caudal displacement of the diaphragm in both mouse and rat models, with an accompanying thorax widening observed exclusively in mice. Increasing PEEP levels in mice and rats was associated with measurable increases in lung volume, with values rising from 12.7 milliliters at zero PEEP to around 15.8 milliliters at six-centimeter water PEEP.