Volume Flow Rate (VFR) Calculation

This second calculation allows the amount of (typically) blood flowing through vessels to be calculated from a phase-contrast angiography image.

In this example, we will use a single axial slice phase-contrast angiogram through the neck to calculate the volume flow rate (VFR) in a carotid artery and a jugular vein. An MRI phase-contrast angiography sequence results in both a magnitude image and a phase image; the phase image is used to calculate the blood flow velocities, but we will use the magnitude image to outline the artery and vein.

The phase image is shown as a movie below.

(Animated: View cine on-line version)

Phase images have intensity ranges that map to phase changes of +π .. -π. The actual intensity values that map to this phase range can be -4096 .. +4096 (typical of images from Siemens MRI scanners), 0 .. +4096 or -3142 .. +3142 (typical of Philips images). Jim can automatically convert from the image intensity values to phase values.

We will outline the artery and vein on a few of the magnitude cine frames, propagate the ROIs to all time points and then go on to calculate the VFR.

Having loaded the magnitude image into Jim's main display, we launched the ROI Propagation toolkit and, using Spline ROIs, outlined one of the carotid arteries and one of the jugular veins at 3 time points: at the beginning and end of the cardiac cycle, and one point around systole. One of these time points is illustrated below:

Phase-contrast angiogram magnitude image, with carotid artery and jugular vein outlines shown at one of the time-points

For ROI propagation across all time points, we used the settings:

• Number of shape coefficients = 6. The vessels have a fairly simple outline shape, and 6 shape coefficients is enough to capture the variations in shape.
• Changes are periodic with time. This is an E.C.G. triggered cine sequence, where the last image frame joins back to the first at the end/start of the cardiac cycle.
• The number of time coefficients was not set manually.

This resulted in good outlining of the artery and vein at all time points, as shown in the movie below.

Calculating the VFR

We will now go on to calculate the VFR of the vessels. Select the 'VFR' tab in the 'Propagated ROI Calculations' panel:

Then set up for VFR calculation:

• If your image is already a velocity map (i.e., the conversion from phase to velocity has already been done) then select .

• Set the phase image (or velocity map) in the "Phase image" selection panel.

• (Optional) Set the magnitude image in the "Magnitude image" selection panel. You do not normally have to select the magnitude image here. However, if you work with images from a General Electric MRI scanner, then you will need to select the magnitude image; this is needed in most cases to correctly convert from phase image pixel values to flow velocity.

• Set either the R-R interval, or the time between individual frames of the angiogram image. If you want Jim to get the time between individual frames from the phase image, then select the check-box. If Jim cannot find the time between frames from the image, then it will give an error, and direct you to set the value manually.

• Set the velocity encoding factor (VENC) for the angiogram. The VENC is the maximum flow velocity that can be encoded without phase wrap.

• Phase correction using a region of stationary tissue. Due to machine imperfections, there may be a constant phase offset in all tissues. If you want to correct this, the phase offset can be measured in stationary tissue, where the intensity in the phase image should correspond to zero phase. Place one or more ROIs on a region of stationary tissue, and save the ROIs into a separate ROI file. Select the check-box, then select that ROI file below.

• . Select this if the phase image suffers from phase wrap and you want Jim to try to correct this automatically. Phase wrap happens when the flow velocity is outside the expected range, and consequently the phase values stray outside the range -π .. +π. The movie image below shows phase wrap in the carotid arteries.

(Animated: View cine on-line version)

If you want to identify the regions of interest, you can do this by providing ROI annotation to the ROIs at any of the time time points. If you provide annotation at multiple time points, the annotation chosen with be that found at the first annotated time point. In the example below we have used the annotation "Jugular" and "Carotid" to identify two vessels.

Click the button to start the VFR calculation.

Two graphs showing the average flow velocities and the volume flow rates through each ROI then pop up:

Then a dialog pops up with a report on the calculated volume flow rate:

The dialog shows:

• The mean and peak flow velocity (through the cardiac cycle) for each of the ROIs. Note that these velocities are averaged over the whole ROI.
• The mean and peak volume flow rate (VFR) for each of the ROIs.

Note: the sign of the flow velocity/VFR indicates the direction of flow relative to the velocity encoding gradient. In the example above, positive values indicate flow towards the head, and negative values indicate flow towards the feet.

You can:

• Write to a text file report. A File chooser will appear, for you to choose a log file name. The default file extension for log files is ".log". If the chosen file already exists, an entry will be appended to the log file.
• Write to a PDF file report. A File chooser will appear, for you to choose a PDF file name. If the chosen file already exists, an entry will be appended to the PDF file.
• Send a PDF report to a DICOM server. The DICOM server to which it will be sent must already have been set up, and is the current server selected in the DICOM Query/Retrieve tool. See these instructions for how to set up the connection to remote DICOM servers.
• Save PDF and Send to DICOM. Both save to disk and send to a DICOM server.