Jun 09, 2026
Slow flowing MRI phantom for FLAIR validation
- 1Fred Hutchinson Cancer Center
Protocol Citation: Brianna France, Elena Carlson 2026. Slow flowing MRI phantom for FLAIR validation. protocols.io https://dx.doi.org/10.17504/protocols.io.3byl4ppnzlo5/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: May 18, 2026
Last Modified: June 09, 2026
Protocol Integer ID: 317289
Keywords: MRI, preclinical imaging, phantom, FLAIR, flow phantom, pump, mri phantom for flair validation, flowing mri phantom, flair imaging performance, measurements in preclinical mri, preclinical mri, assessing flair signal suppression, mouse head coil, optimizing flair acquisition parameter, flair acquisition parameter, flair signal suppression, flair validation, chamber to an external syringe pump
Funders Acknowledgements:
National Institutes of Health
Grant ID: P30 CA015704
National Institutes of Health
Grant ID: S10OD26919
Abstract
This work presents a compact, MRI‑compatible flow phantom developed to validate FLAIR imaging performance under controlled conditions. The phantom consists of a 0.1 mM contrast‑filled syringe housed within a modified 15 mL tube and positioned inside a mouse head coil to match small‑animal imaging geometry. Inflow and outflow tubing connect the chamber to an external syringe pump, enabling stable, low‑rate fluid motion while keeping all magnetic‑sensitive components outside the scanner. The system provides a reproducible environment for assessing FLAIR signal suppression, uniformity, and flow‑related artifacts. This setup offers a practical platform for optimizing FLAIR acquisition parameters and improving confidence in FLAIR‑based measurements in preclinical MRI.
Attachments
Image Attribution
Schematics were all created in biorender
Materials
36" IV Extension Set with smallbore tubing. Priming volume Approx. 0.8 mL, DYNDTN0009
10mL Syringe, diameter 14.5mm, Area 0.253 In^2, BD Luer Lock Tip, 302995
15mL Centrifuge Tubes, 430053
Harvard Apparatus PHD Ultra Syringe Pump
Safety warnings
All components inside the bore must be non‑magnetic
Step-by-step MRI Flow Phantom Construction
Schematic
Prepare the contrast syringe by filling a 0.5-1 mL syringe with 0.1 mM contrast solution (commonly Gd‑based diluted in saline).
Remove all bubbles by gentle tapping and slow plunger advancement.
Replace cap to keep the system closed, cut off plunger.
Build the phantom chamber by cutting the bottom off a 15 mL conical tube to create a cylindrical housing.
Attach inflow and outflow tubing to the contrast filled syringe and insert horizontally so it sits centered within the tube.
Ensure the syringe is fully supported and cannot rotate with tape.
Connect catheter tubing to the second catheter extension that will be attached to the syringe (inflow).
Connect a second tube to the opposite end (outflow).
Confirm both lines are straight and free of kinks to avoid flow artifacts.
Note tube flow directions!
Place the 15 mL tube (with syringe and flow tubes inside) into the mouse head coil.
Align the syringe barrel with the coil’s isocenter to ensure uniform sensitivity.
Secure with clay or tape so the phantom cannot shift during scanning.
Set up the syringe pump outside the MRIs gauss line.
Load a 10 mL syringe filled with water onto the pump.
Connect inflow catheter tubing to filled syringe.
Connect the outflow tubing to a 15 mL waste tube. A hole was created in the lid.
Position the waste tube safely away from the coil and electronics.
Ensure gravity does not create back‑pressure — keep the waste tube at or below the phantom height.
Prime the system by running the pump at a slow rate (e.g., 0.1–0.3 mL/min) until fluid reaches the waste container.
Watch for bubbles; if present, flush until the flow path is completely air‑free.
Confirm the tubes surrounding the contrast syringe fills smoothly and no leaks occur.
This ideally is teasted before placing in the scanner.
Calculating the correct flow rate for the pump settings
Calculating the correct flow rate to use to get 300 micrometers per second velocity in the catheter tubing for the phantom
We calculated the pump's setting and flow rate using continuity equation (Q=A*v) for incompressible flow
The flow rate Q (in cubic micrometers per second) is the same between both cylinders.
Q1 = Q2
Q=A*v
So if the smaller tube has area A2, its velocity is:
v2=A1*v1/A2
Assemble the Flow PathSetup
Ensure the syringe and catheter extensions are connected exactly as they will be during the experiment.
Attach the 10 mL syringe to the pump.
Connect the two 36-inch catheter extensions in series.
Confirm the total priming volume is 1.6 mL (1600 mm³). This is the amount of water held by the two cathethers when connected together.
Verify total catheter length is 1828.8 mm.
Calculate Catheter's Cross‑Sectional Area
Determine the internal area needed to compute volumetric flow rate.
A = Volume / Length
A = 1600 mm³ / 1828.8 mm = 0.875 mm²
Use the measured priming volume and total catheter length.
Record the calculated area for later use.
Convert Desired Flow Velocity
Convert the physiological CSF velocity into consistent units.
Desired CSF velocity: 300 µm/s.
Convert to millimeters per second: 300 µm/s = 0.3 mm/s.
Use this value in the flow equation.
Compute Volumetric Flow Rate Formula
Q = v × A
Q = (0.3 mm/s)(0.875 mm²) = 0.2625 mm³/s
Since 1 mm³ = 1 µL, the final flow rate is:
Q = 0.2625 µL/s.
This is the pump setting required to achieve the target CSF velocity within the catheter tubes.
Imaging
Fast Spin Echo sequence on the phantom
FLAIR sequence on the phantom
Protocol references
Li J, Pei M, Bo B, Zhao X, Cang J, Fang F, Liang Z. Whole-brain mapping of mouse CSF flow via HEAP-METRIC phase-contrast MRI. Magn Reson Med. 2022 Jun;87(6):2851-2861. doi: 10.1002/mrm.29179. Epub 2022 Feb 2. PMID: 35107833; PMCID: PMC9305925.
Acknowledgements
This research was supported by the Preclinical Imaging Shared Resource (RRID:SCR_022616 ) of the Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium (P30 CA015704) and the 3T/7T MRI Shared Instrumentation Grant NIH S10OD26919.