• Specifications
• ExperimentationAnatomicalImaging

-- ["aerdemir"] DateTime(2014-06-25T12:39:05Z) This specification is asking for input from the community. Please provide your feedback

• by editing the ["/Discussion"] page, or

• by responding to relevant [https://simtk.org/forums/viewtopic.php?f=485&t=4996 forum entry], or

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TableOfContents

Target Outcome

A set of magnetic resonance (MR) images of the knee specimen with clear visual delineation of tissue boundaries, including: the bones (femur, tibia & patella), cartilage, meniscii (medial & lateral), ligaments (ACL, PCL, MCL, LCL & patellar) and tendon (quadriceps).

Prerequisites

Infrastructure

• ["Infrastructure/ExperimentationImaging"]

Prerequisite Protocols

• ["Specifications/Specimens"]
• ["Specifications/SpecimenPreparation"]
• ["Specifications/Registration"]

Procedure

Schedule Imaging Session

Contact the MRI technician at University Hospitals, Case Medical Center to arrange a time to acquire the MR images. This should be initiated X weeks prior to the desired imaging date.

MRI Technician: Shannon Donnolla BR Email: sbd39@case.edu BR Phone: 216-844-8054

Additional information about the imaging facility, all associated contacts, and MRI hardware can be found at:

• ["Infrastructure/ExperimentationImaging"]

Place Specimen in Transport Container

To accomplish this task, the following tools/supplies will be required:

• transportation tube
• permanent marker
• hemostats
• medical scissors
• scalpel
• ruler
• biohazard bag
• tape to secure the transportation tube
• scissors to cut the tape
• chucks for specimen preparation
• duffel bag

ImageLink(https://simtk.org/svn/openknee/doc/img/Transportation_Tools.png, width=300, alt=Experimentation Workflow)

The following image describes the workflow to prepare the specimen for transport to the imaging facility (description below):

ImageLink(https://simtk.org/svn/openknee/doc/img/Transportation_Process.png, width=700, alt=Experimentation Workflow)

1. Get the transport container, which consists of a transparent acrylic tube (outer diameter [OD] = 6", inner diameter [ID] = ~5,3/4", length = 20") divided into two hemi-cylindrical halves, one of which has fused end caps (A).
2. The knee is supported along the central axis of the tube with 1" thick foam disks that can be independently positioned along the length of the tube with velcro to account for specimens of varying length (B).
   • The hemi-cylindrical cap of the transport tube can be used to "dry-fit" the foam supports onto the specimen.

3. Insert either end of the specimen (i.e. the cut ends of the diaphyses of the femur and tibia) into appropriately sized and positioned holes in the foam disks (i.e. foam "potting") to ensure that the specimen lies along the axis of the transport tube in neutral flexion (C & D).

4. Through a horizontal incision in the foam disks on the femoral side (at an appropriate distance from the femur to ensure proper line of action), pull the patellar tendon through with a hemostat until a tension is applied that ensures the patellar ligament is not slack (kinked) between the patellar and tibial insertions (E).
5. Make a small incision (or two) in the patellar tendon, at the point where it exits the hole on the outermost edge of the foam disk.
6. Pass a zip tie through each hole in the tendon.
7. Then pass other zip ties through each of the zip ties in the tendon, to prevent the patellar tendon from pulling back through the foam disk to hold the desired tension.
8. Estimate the clearance around the epicondylar axis at neutral flexion (ensuring it is not hyperextended) and cut a complementary shape from a hemicircular piece of foam to support the posterior surface of the knee at the joint (C).
9. Velcro the central foam support at the center of the transport tube.
10. Velcro the "foam-potted" specimen into the transport tube with the patella facing upwards, and the posterior surface of the tibiofemoral joint resting on a foam support at the center of the tube (minimizes the potential for deflection of the registration markers) (F).
11. Ensure the knee is secure and level in the transport tube (G).
12. Double check to ensure the knee is secure and level in the transport tube.
13. After inserting the specimen in the transport tube, secure the hemi-cylindrical cap in place with (weak) tape (H).
14. Place the transport tube into a large biohazard bag to prevent contamination of MRI imaging facilities at Case (I). WARNING: The outside of the bag must not be contaminated while placing the transport tube inside!!! To do so requires two individuals, one who is contaminated and inserts the transport tube in the biohazard bag and only touches its interior (the "dirty handler"), and the other with clean gloves who only touches the non-contaminated exterior of the bag (the "clean handler").
15. Zip tie the biohazard bag closed and cut the excess bag and zip tie material with scissors.
16. Mark the location of the patella and the femoral (superior) direction with a permanent marker to ensure the specimen is placed in the MRI machine with the desired orientation.
17. Get the duffel bag is used to carry the transport tube between the Clinic and Case, which is stored in the lower drawer of the filing cabinet at Jason's desk. WARNING: This bag must also not be contaminated and should be placed on a chair if it is in the biorobotics room, not the floor!!!
18. Place the biohazard bag containing the transport tube into the duffel bag with the patella facing upwards for transport.

Transport Specimen

The knee specimens will be transported between The Cleveland Clinic and University Hospitals, Case Medical Center for MR imaging in the transport container. Maybe describe relevent parking/location information at Case?

Position/Orient Specimen in MRI Machine

Within the transport tube, the specimen will be oriented with the patella directed upwards so the posterior surface of the tibiofemoral joint rests on the central foam support (see figure above). For alignment in the MRI, the femur side of the tube will be clearly marked on the outside of a plastic bag containing the tube. The femur, with the patella facing upwards, will be inserted into the scanner first, which corresponds to a supine position of a patient (i.e. head first into the scanner).

Acquire Image Sequences

For each knee, the following set of image collection protocols will be performed. All images should be acquired in the same coordinate system to be able to align reconstructed tissue geometries during assembly of full knee geometry. To accomplish this the origin (isocenter) and the axes of the magnet, which is set at the beginning of the session, should not change. In addition, the specimen should not be moved. It should be noted that a pixel-by-pixel alignment of image sets (co-localization) is not necessary.

The imaging protocols were initially based on OAI protocols from [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048821/ Peterfy et al. (2008)]. Multiple iterations were performed to finalize the protocols to match the needs of Open Knee(s); see ["/Discussion"] for more details.

Before, each sequence is acquired, verify that the acquisition properties match the desired settings in the tables below. After each sequence is acquired, inspect the images and compare them against the sample images below to to ensure that it was collected properly. If not, the sequence should be recollected.

SETTINGS 1: SPECIMEN LOCATORS

Multiple images sets will be acquired for localization of region of interest on a need basis.

SETTINGS 2: GENERAL PURPOSE IMAGING

The goal of this imaging protocol is to acquire an isotropic image volume with a voxel size of 0.5 mm x 0.5 mm x 0.5 mm or smaller and with a large field of view inclusive of both tibiofemoral and patellofemoral joints and registration markers. This image set will likely be utilized for geometric reconstruction of registration markers. It may also support geometric reconstruction of other tissue structures.

Sequence #1: 3D T1-weighted without fat suppression - isotropic voxel size

Sample Image Sequence Identifier: t1_fl3d_sag_p2_iso_0.4_we (relevant protocol name used by the imaging facility at the University Hospitals)

Sample Image Acquisition Properties:

Sample Image Header: attachment:t1_fl3d_sag_p2_iso_0.4_we.txt

Sample Image:

attachment:t1_fl3d_sag_p2_iso_0.4_we.png

Sample image information is from a scan acquired on March 4, 2014, also see ["/Discussion"].

SETTINGS 3: CARTILAGE IMAGING

The goal of this imaging protocol is to acquire an image set with sagittal plane resolution of approximately 0.35 mm, an out-of-plane resolution of approximately 0.7 mm and a large enough field of view inclusive of both tibiofemoral and patellofemoral cartilage. This image set will likely be utilized for geometric reconstruction of cartilage. It may also support geometric reconstruction of other tissue structures.

Sequence #2: 3D T1-weighted with fat suppression - anisotropic voxel size

Sample Image Sequence Identifier: t1_fl3d_sag_350x350x700_fs (relevant protocol name used by the imaging facility at the University Hospitals)

Sample Image Acquisition Properties:

Sample Image Header: attachment:t1_fl3d_sag_350x350x700_fs.txt

Sample Image:

attachment:t1_fl3d_sag_350x350x700_fs.png

Sample image information is from a scan acquired on March 20, 2014, also see ["/Discussion"].

SETTINGS 4: CONNECTIVE TISSUE IMAGING

The goal of this imaging protocol is to acquire axial, sagittal, and coronal plane image sets with an in-plane resolution of approximately 0.35 mm, an out-of-plane resolution of approximately 2.8 mm (1.4 mm slice thickness and 1.4 mm gap) and a large enough field of view inclusive of collateral and cruciate ligaments, quadriceps tendon and patellar ligament. This image set will likely be utilized for geometric reconstruction of ligaments. It may also support geometric reconstruction of other tissue structures.

Sequence #3: MESE type - axial plane

Sequence #4: MESE type - sagittal plane

Sequence #5: MESE type - coronal plane

Sample Image Sequence Identifier: pd_tse_sag_1.4mmslice_1avg (relevant protocol name used by the imaging facility at the University Hospitals)

Sample Image Acquisition Properties:

Sample Image Header: attachment:pd_tse_sag_1.4mmslice_1avg.txt

Sample Image:

attachment:pd_tse_sag_1.4mmslice_1avg.png

Sample image information is from a scan acquired on March 20, 2014, also see ["/Discussion"].

Obtain and Store Image Data

MR image files (DICOM format) will be provided by the MRI technician following image acquisition and transferred to an external hard drive provided by Open Knee(s) personnel. The MR image files can be renamed to easily identify which image files belong in a sequence using a MATLAB script (dicomrename.m, [https://simtk.org/websvn/wsvn/openknee/utl/mri/#_utl_mri_]). The Open Knee(s) personnel will upload the original and renamed MRI image data files to the in-house data management system (http://cobicore.lerner.ccf.org/midas, accessible only within the Cleveland Clinic network) for prospective organization (Open Knee(s) Community). Following organization, a documented version of the data will be disseminated at Open Knee(s) project site (https://simtk.org/home/openknee).

Store Specimen

After transporting the specimen back to the Clinic from the imaging facility at University Hospitals, the specimen should be stored according to storage specifications listed in the specimen preparation page, see ["Specifications/SpecimenPreparation"].

References

Peterfy CG, Schneider E, Nevitt M. The osteoarthritis initiative: report on the design rationale for the magnetic resonance imaging protocol for the knee. Osteoarthritis Cartilage. 2008 Dec;16(12):1433-41. [http://www.ncbi.nlm.nih.gov/pubmed/18786841 PubMed]