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 Sets

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.

PROTOCOL 1: SPECIMEN LOCATORS

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

PROTOCOL 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.

Image Sequence Type: 3D T1-weighted without fat suppression - isotropic voxel size

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

Sample Image Acquisition Properties:

Sample Image Header:

Sample Image:

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

PROTOCOL 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.

Image Sequence Type: 3D T1-weighted with fat suppression - anisotropic voxel size

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

Sample Image Acquisition Properties:

Sample Image Header:

Sample Image:

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

PROTOCOL 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.

Image Sequence Type: MESE type - axial plane

Image Sequence Type: MESE type - sagittal plane

Image Sequence Type: MESE type - coronal plane

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

Sample Image Acquisition Properties:

Sample Image Header:

Sample Image:

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 Open Knee(s) personnel will upload the MRI data 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 the [:Specifications/SpecimenPreparation#Specimen_Storage:Specimen Storage] specifications listed in the specimen preparation page.

-- ["aerdemir"] DateTime(2014-04-01T13:49:45Z) The results of imaging trials and the discussions below are currently under organization.

Acquire Image Sequences

For each knee, the following set of image sequences will be performed. Coordinate systems for all 3D image sets will be aligned, so that the geometry for the structures of interest can be defined from the appropriate sequence and combined into a single model.

OAI protocols are from [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048821/ Peterfy et al. (2008)]. Open Knee(s) image settings do not need to be exactly as in OAI protocols. OAI protocols provide a good starting point to acquire adequate contrast for reconstruction of tissue geometry. Desirable in-plane resolution of images should be less then 0.5 mm and image thickness+gap should be less than 1-1.5 mm. Per Chris Flask (of the imaging facility) MESE sounds like a spin echo acquisition. DESS seems to be a vendor-specific acquisition, basically a T2 weighted image acquisition. His interpretation of T1-ISO, DESS, and MESE are T1-weighted acquisition, T2-weighted acquisition with fat suppression, maybe a proton density weighted acquisition.

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.

In a potential publication, the reporting of the imaging (for geometry reconstruction) will sound like:

We acquired 3 image sets from the same cadaver knee specimen. The imaging specifications included a T1-weighted iso protocol (0.5 mm voxel resolution) along with two other protocols OAI settings reported for DESS (sagittal: # in plane resolution, # slice thickness and gap) and MESE (axial: # in plane resolution, # slice thickness and gap). Different image sets were used to reconstruct actual geometries of tissues. As the DICOM coordinate system was the same and the specimen did not move between scans, the geometries are already registered to each other, i.e., they are defined in the same coordinate system. The geometries were then assembled in a computer aided design package to reconstruct the geometric representation of the whole knee.

SEQUENCE 1: T1-ISO

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 and bones. It may also support geometric reconstruction of other tissue structures.

• Contrast Type: T1-weighted

• Scanning Sequence: Gradient Echo (GR)

• Acquisition Type: 3D (=> isotropic)

• Resolution: 0.5 mm, isotropic

• Repetition time (TR): 20 ms

• Echo time (TE): 4.92 ms

• Flip angle: 25 degrees

• Scan Time: Approximately 17 minutes

These settings were extracted from the DICOM header of a previous imaging session (CoBi Core project CBC_0049/01/dat/MRI/knee1?). This protocol has been used to create an isotropic, T1-weighted image set that reasonably represented the structures of interest, namely cartilage, soft-tissue and an outline of the bony anatomy.

attachment:MRI_Settings_T1.txt

EXAMPLE IMAGES

Axial:

attachment:knee_AXL.png

Sagittal:

attachment:knee_SAG.png

Coronal:

attachment:knee_COR.png

SEQUENCE 2: DESS-APPROX

The goal of this imaging protocol is to acquire a sagittal plane image set with an in-plane resolution less than 0.5 mm, an out-of-plane resolution less than 1.5 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 menisci.

• Contrast Type: Double-Echo Steady-State (DESS), T1-weighted

• Scanning Sequence: Gradient Echo (GR)

• Sequence Variant: SP\OSP

• Scan Options: SAT1\WE

• Acquisition Type: 3D

• Slice Orientation: sagittal

• Resolution (in-plane): 0.36 x 0.36 mm (sagittal)

• Slice Thickness: 0.70 mm

• Repetition time (TR): 16.3 ms?

• Echo time (TE): 4.78 ms?

• Number of Averages: 1

• Imaging Frequency: 123.25643

• Flip angle: 25 degrees

• Field of View: 140.0 x 140.0 mm (384 x 384 pixels)

• Scan Time: 15.28 minutes?

EXAMPLE IMAGE

Sagittal:

attachment:DESS_approx_SAG.png

SEQUENCE 3: MESE-APPROX

The goal of this imaging protocol is to acquire an axial plane image set with an in-plane resolution less than 0.5 mm, an out-of-plane resolution less than 1.5 mm 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 menisci.

Additional Information

Handling of Imaging Artifacts

References

Notes from Previous Explorations

QUESTIONS FOR CARL WINALSKI -- ["craigbennetts"] DateTime(2013-11-11T22:29:59Z)

1. Is there a trade-off between image resolution, image acquisition (2D or 3D), and the contrast between structures for certain acquisition settings?
2. What are the best acquisition settings to provide a single image set with good overall delineation of cartilage, meniscus, tendon, ligament, bone boundaries? In the past, we have used the following settings: 3D (isotropic, 0.5 mm), Gradient Echo, T1-weighted

General MRI Info

Following is an overview of relevant imaging sequences and their suitability for visualizing different anatomical structures of the knee. Candidate MR sequences and approaches to overcome metal artifact were found in the literature. Some references were focused on specific structure, e.g. cartilage, and may be suitable for semi-automatic (or even automatic) segmentation of that specific structure.

Cartilage: 1) gradient echo, with or without fat suppression, 2) spin echo, with fat suppression

Meniscus: Proton density

Ligaments/tendons: T2-weighted

Grenier JM, Green N, Wessley, MA. Knee MRI. Part 1: basic overview. Clinical Chiropractic, 2004, 7:84-89. [http://www.sciencedirect.com/science/article/pii/S1479235404000197# Science Direct Link]

3D gradient echo: good for cartilage

3D spin echo: good for cartilage, ligaments, meniscus

Subhas N, Kao A, Freire M, Polster JM, Obuchowski NA, Winalski CS. MRI of the Knee Ligaments and Menisci: Comparison of Isotropic-Resolution 3D and Conventional 2D Fast Spin-Echo Sequences at 3T. American Journal of Roentgenology, 2011, 197:442-450. [http://www.ncbi.nlm.nih.gov/pubmed/21785092 PubMed Link]

Techniques for reducing metal artifacts:

Stradiotti P, Curti A, Castellazzi G, Zerbi A. Metal-related artifacts in instrumented spine. Techiques for reducing artifacts in CT and MRI: state of the art. European Spine Joural, 2009, 18(Suppl 1):S102-S108. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2899595/ NCBI Link]

An approach for automatic segmentation of cartilage.

In this study, 20 healthy volunteers were used to evaluate the accuracy of an approach for automatic segmentation of cartilage.

A quote from the study outlines their imaging sequences:

"The MR images were acquired using three different sets of parameters. Several parameters were common, with all images acquired in the sagittal plane with a field of view (FOV) 120 mm, slice thickness 1.5 mm, and repetition time (TR) 60 ms. A flip angle of 40° was used on all cases except case 7 which used 30°. Six scans were acquired at 3 T with in-plane spacing 0.23 × 0.23 mm and echo time (TE)7 ms. A birdcage coil was used for 5 of these scans (cases 1, 6, 14, 15, 16) and a head coil was used on case 3. Fourteen scans were acquired at 1.5T using two different extremity array coils. A G.E. coil was used for five of the scans with image matrix with in-plane spacing 0.46 × 0.46 mm, TE5 ms used for four cases (cases 17, 18, 19, 20), while case 7 was acquired with in-plane spacing 0.23 × 0.23 mm, TE3.2 ms, and flip angle 30°. A MEDRAD coil was used for the other nine images with in-plane spacing 0.23 × 0.23 mm, TE 7 ms (cases 2, 5, 8, 10, 12, 13), and 12 ms (cases 4, 9, 11)."

The reference can be found here: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717377/]

Imaging Trial 5: March 20, 2014

Proposed scans

1. Obtain a 3D T1-weighted image set with fat suppression.
   • Protocol: t1_fl3d_sag_p2_iso_0.4_fs
     • Plane: 3D
     • Desired resolution: 0.3409 x 0.3409 x 0.7 mm
   Notes: Previously an isotropic image set was collected with 0.5 mm x 0.5 mm x 0.5 mm voxels. For this set may be the voxel size can be made anisotropic with increased resolution in sagittal plane yet decreased resolution out-of-plane. This will be compared with other cartilage imaging modalities that were already collected. It will help us see if we establish the boundaries of the cartilage any better.
2. Obtain multi-plane MESE type images:
   • Protocol: pd_tse_cor_p2_384
     • Plane 1: Sagittal
     • Desired resolution: 0.3409 x 0.3409 x 3.0 mm thickness (no gap)
   • Protocol: pd_tse_cor_p2_384
     • Plane 2: Axial
     • Desired resolution: 0.3409 x 0.3409 x 3.0 mm thickness (no gap)
   • Protocol: pd_tse_cor_p2_384
     • Plane 3: Coronal
     • Desired resolution: 0.3409 x 0.3409 x 3.0 mm thickness (no gap)
   Notes: Previously collected these image sets in sagittal and axial planes. Acquiring a coronal image set may help inreconstruction of collateral and cruciate ligaments.
3. Obtain multiple MESE type images with different # of excitations and thickness:
   • Protocol: pd_tse_cor_p2_384
     • Plane: Sagittal
     • Desired resolution: 0.3409 x 0.3409 x 1.0 mm thickness (2 mm gap)
     • # of excitations: 1
   • Protocol: pd_tse_cor_p2_384
     • Plane: Sagittal
     • Desired resolution: 0.3409 x 0.3409 x 1.0 mm thickness (2 mm gap)
     • # of excitations: 3
   Note: With 3 mm thick slices some averaging artifacts are seen. 1 mm thick slices (with 2 mm gap) may look any better. The increased # of excitations may accommodate SNR issues related to thinner slices.

Results

-- ["aerdemir"] DateTime(2014-03-23T13:25:18Z) Scan numbers are based on the order of the imaging as implemented in MRI session. Scans 1 & 2 were localizers.

SCAN 3

• Protocol name. pd_tse_axial_p2_384

• Goal. An axial plane MESE-type scan with approximately 0.35 mm x 0.35 mm x 3 mm (slice thickness)

attachment:scan_3_HEADER_03.20.14.txt

attachment:pd_tse_axial_p2_384.png

SCAN 4

• Protocol name. pd_tse_sag_p2_384

• Goal. A sagittal plane MESE-type scan with approximately 0.35 mm x 0.35 mm x 3 mm (slice thickness)

attachment:scan_4_HEADER_03.20.14.txt

attachment:pd_tse_sag_p2_384.png

SCAN 5

• Protocol name. pd_tse_cor_p2_384

• Goal. A coronal plane MESE-type scan with approximately 0.35 mm x 0.35 mm x 3 mm (slice thickness)

attachment:scan_5_HEADER_03.20.14.txt

attachment:pd_tse_cor_p2_384.png

SCAN 6

• Protocol name. pd_tse_sag_1.4mmslice_1avg

• Goal. A sagittal plane MESE-type scan with approximately 0.35 mm x 0.35 mm x 1.4 mm (slice thickness) + 1.4 mm (gap); number of excitation = 1 (slice thickness is a limiting factor)

attachment:scan_6_HEADER_03.20.14.txt

attachment:pd_tse_sag_1.4mmslice_1avg.png

SCAN 7

• Protocol name. pd_tse_sag_1.4mmslice_3avg

• Goal. A sagittal plane MESE-type scan with approximately 0.35 mm x 0.35 mm x 1.4 mm (slice thickness) + 1.4 mm (gap); number of excitation = 3

attachment:scan_7_HEADER_03.20.14.txt

attachment:pd_tse_sag_1.4mmslice_3avg.png

SCAN 8

• Protocol name. t1_fl3d_sag_350x350x700_fs

• Goal. A 3D T1-weighted image set with fat supression with higher resolution in sagittal plane, approximately 0.35 mm x 0.35 mm x 0.7 mm

attachment:scan_8_HEADER_03.20.14.txt

attachment:t1_fl3d_sag_350x350x700_fs.png

SCAN 9

• Protocol name. t1_fl3d_sag_350x350x700

• Goal. A 3D T1-weighted image set without fat supression with higher resolution in sagittal plane, approximately 0.35 mm x 0.35 mm x 0.7 mm

attachment:scan_9_HEADER_03.20.14.txt

attachment:t1_fl3d_sag_350x350x700.png

Imaging Trial 4: March 4, 2014

-- ["hallorj"] DateTime(2014-03-04T15:59:15Z) add exact protocol names, provided by the UH imaging resource, from the DICOM headers for each sequence below. This should facilitate use of the correct sequence during the imaging sessions.

Attendees: Chris, Shannon (UH); Ahmet, Craig, Snehal (CC)

The goal of this imaging trial was to conduct a full mock-up imaging of a knee specimen including:

• 2 T1-weighted, isotropic (0.5mm) images (based on CoBi Core's previous protocols)

  • with fat suppression (= WE = Water Excitation)
  • without fat suppression (t1_fl3d_sag_p2_iso_0.5)
• 2 DESS-type, sagittal plane images (~0.3x0.3x0.7):
  • DESS-APPROX sequence (based on the settings from Nov. 14, 2013)
  • T2 spin echo (suggested by Chris to replicate OAI DESS image contrast).
• 3 MESE-type, axial plane image sets: (slice thickness = 3mm)
  • MESE (OAI protocols)
  • Turbo Spin Echo (TSE) (to replicate OAI MESE image contrast).

Results

DICOM ORDER #4) T1-ISO WITHOUT FAT SUPPRESION:

attachment:T1_iso_HEADER_03.04.14.txt

Series Description: t1_fl3d_sag_p2_iso_0.4_we

Resolution: 0.5 x 0.5 x 0.5 mm

attachment:T1_iso_AXL_03.04.14.png attachment:T1_iso_SAG_03.04.14.png attachment:T1_iso_COR_03.04.14.png

Notes from Imaging Session

This imaging sequence corresponded to Scan 3 of the whole protocol as it was setup in the MRI machine. It was intended to be a T1-weighted isotropic imaging (flash 3D without fat suppression) with 0.5 mm x 0.5 mm x 0.5 mm voxel size. The femur was placed through the bore first (head first). Images are misoriented as it was assumed that the tibia was placed through the bore first during direction setup (feet first). In future imaging sessions, the team needs to ensure that femur goes first and inform the imaging personnel so that appropriate orientation is set up.

Sequence name: t1_fl3d_sag_p2_iso_0.4_we FOV (mm): 240 mm read x 65.8% --> 158 x 158 x 240 TR (ms): 20 TE (ms): 6.01 # of slices: 320 Flip angle (deg.): 25 Bandwidth (Hz/pixel): 210 Chemical Shift (pixels): No. excitations averaged: 1 ETL: 1 Phase encode axis: A/P Distance factor (%): 0 (irrelevant for 3D) Phase oversampling: 0 Slice oversampling: 0 Phase/slice/read resolution: 500 um (?) Slice partial Fourier: 7/8 Phase partial Fourier: 1 (?) Readout partial Fourier: 1 (?) X-resolution (mm): 0.5 Scan time (min.): ~21

DICOM ORDER #5) T1-ISO WITH FAT SUPPRESION:

attachment:T1_iso_fs_HEADER_03.04.14.txt

Series Description: t1_fl3d_sag_p2_iso_0.4_fs

Resolution: 0.5 x 0.5 x 0.5 mm

attachment:T1_iso_fs_AXL_03.04.14.png attachment:T1_iso_fs_SAG_03.04.14.png attachment:T1_iso_fs_COR_03.04.14.png

Notes from Imaging Session

This imaging sequence corresponded to Scan 4 of the whole protocol as it was setup in the MRI machine. It was intended to be a T1-weighted isotropic imaging (flash 3D with fat suppression) with 0.5 mm x 0.5 mm x 0.5 mm voxel size. All imaging settings are essentially the same as those of without fat suppression (see immediately above).

Sequence name: t1_fl3d_sag_p2_iso_0.4_fs

DICOM ORDER #6) DESS-TYPE (BASED ON OAI):

attachment:DESS-APPROX_HEADER_03.04.14.txt

Series Description: dess_3dsag_we

Resolution: 0.3409 x 0.3409 x 0.7 mm

attachment:DESS-APPROX_SAG_03.04.14.png

Notes from Imaging Session

This imaging sequence corresponded to Scan 5 of the whole protocol as it was setup in the MRI machine. It was intended to reproduce DESS imaging protocol from the OAI study. The goal was to obtain a sagittal image set with ~0.35 mm x ~0.35 mm in plane resolution and 0.7 mm image thickness (no gap). Note that this is NOT T2 spin echo, it is as close as it gets to OAI. A T2 spin echo may be brighter in the cartilage.

Sequence name: dess_3dsag_we FS: Yes (-- ["aerdemir"] DateTime(2014-03-10T12:02:30Z) I assume WE.) Plane: Sagittal FOV (mm): 240 mm read (H/F) x 62.5% (A/P) --> 240 mm x 150 mm x 150 mm Slice thickness/gap (mm/mm): 0.7/0 TR (ms): 16.5 TE (ms): 5 # of slices: 160 Flip angle (deg.): 25 Bandwidth (Hz/pixel): 187 Chemical Shift (pixels): No. excitations averaged: 1 ETL: 1 Phase encode axis: Distance factor (%): 0 Phase oversampling: 0 Slice oversampling: 20% Phase/slice/read resolution: Slice partial Fourier: 6/8 Phase partial Fourier: Readout partial Fourier: X-resolution (mm): 240/704 --> 0.3409 Y-resolution (mm): 150/352 --> 0.4261 (-- ["aerdemir"] DateTime(2014-03-10T12:02:30Z) I took a note of '150/352'. I am not sure what it corresponds to.) Scan time (min.): ~14

DICOM ORDER #7) T1 VIBE (DESS-LIKE CONTRAST AND RESOLUTION):

attachment:DESS-type_T1_vibe_HEADER_03.04.14.txt

Series Description: T1_vibe_we_sag_iso_p2_EP

Resolution: 0.3409 x 0.3409 x 0.7 mm

attachment:DESS-type_T1_vibe_SAG_03.04.14.png

Notes from Imaging Session

This imaging sequence corresponded to Scan 6 of the whole protocol as it was setup in the MRI machine. It was intended to be a sagittal image set with ~0.35 mm x ~0.35 mm in plane resolution and 0.7 mm image thickness (no gap). Note that this imaging sequence has been previously referred by the team as DESS-APPROX (see sequence 2 of November 14, 2013 trial). It is actually closer to a T1-weighted imaging sequence with fat supression and can be used to replace DESS-type imaging for cartilage reconstruction.

Sequence name: t1_vibe_we_sag_isop2_EP Plane: Sagittal FOV (mm): 240 mm x 62.5% --> 240 mm x 150 mm x 150 mm Slice thickness/gap (mm/mm): 0.7/0 TR (ms): 12 TE (ms): 6.2 # of slices: 240 Flip angle (deg.): 25 Bandwidth (Hz/pixel): 190 Chemical Shift (pixels): No. excitations averaged: 1 ETL: Phase encode axis: Distance factor (%): 0 Phase oversampling: 0 Slice oversampling: 0 Phase/slice/read resolution: Slice partial Fourier: 6/8 Phase partial Fourier: Readout partial Fourier: X-resolution (mm): 240/704 --> 0.3409 Scan time (min.): ~11.5

DICOM ORDER #8) MESE-TYPE TSE 2D, SAGITTAL (BASED ON OAI):

attachment:MESE-type_TSE_2D_SAG_HEADER_03.04.14.txt

Series Description: pd_tse_cor_p2_384

Sequence Name: *tse2d1_14

Resolution: 0.3409 x 0.3409 x 3.0 mm

attachment:MESE-type_TSE_2D_SAG_03.04.14.png

Notes from Imaging Session

This imaging sequence corresponded to Scan 7 of the whole protocol as it was setup in the MRI machine. It was intended to reproduce MESE imaging protocol from the OAI study. The goal was to obtain a sagittal image set with ~0.35 mm x ~0.35 mm in plane resolution and 3 mm image thickness (no gap).

Sequence name: pd_tse_cor_p2_384 Plane: Sagittal FOV (mm): 240 x 62.5% --> 240 x 150 x 150 Slice thickness/gap (mm/mm): 3/0 TR (ms): 8000 TE (ms): 11 # of slices: 35 Flip angle (deg.): 90 Bandwidth (Hz/pixel): 222 Chemical Shift (pixels): No. excitations averaged: 1 ETL: 14 Phase encode axis: Distance factor (%): 0 Phase oversampling: 0 Slice oversampling: 0 Phase/slice/read resolution: Slice partial Fourier: Phase partial Fourier: Readout partial Fourier: X-resolution (mm): 240/704 --> 0.3409 Scan time (min.): ~4

DICOM ORDER #9) MESE-TYPE TSE 2D, AXIAL:

attachment:MESE-type_TSE_2D_AXL_HEADER_03.04.14.txt

Series Description: pd_tse_cor_p2_384

Sequence Name: *tse2d1_14

Resolution: 0.3516 x 0.3516 x 3.0 mm

attachment:MESE-type_TSE_2D_AXL_03.04.14.png

Notes from Imaging Session

This imaging sequence corresponded to Scan 8 of the whole protocol as it was setup in the MRI machine. It was intended to be an axial image set with ~0.35 mm x ~0.35 mm in plane resolution and 3 mm image thickness (no gap).

Sequence name: pd_tse_cor_p2_384 Plane: Axial FOV (mm): 180 x 75% --> 180 x 135 x 135 Slice thickness/gap (mm/mm): 3/0 TR (ms): 13000 TE (ms): 10 # of slices: 70 Flip angle (deg.): 90 Bandwidth (Hz/pixel): 222 Chemical Shift (pixels): No. excitations averaged: 1 ETL: 14 Phase encode axis: Distance factor (%): 0 Phase oversampling: Slice oversampling: 0 Phase/slice/read resolution: Slice partial Fourier: Phase partial Fourier: Readout partial Fourier: X-resolution (mm): 180/512 --> 0.3516 Scan time (min.): ~5.7

DICOM ORDER #10) MESE-TYPE TSE 2D, AXIAL (STACKED THIN SLICES):

attachment:MESE-type_TSE_3D_AXL_HEADER_03.04.14.txt

Series Description: pd_tse_cor_p2_384

Sequence Name: *tse3d1_14

Resolution: 0.3516 x 0.3516 x 0.7 mm

attachment:MESE-type_TSE_3D_AXL_03.04.14.png

Notes from Imaging Session

This imaging sequence corresponded to Scan 9 of the whole protocol as it was setup in the MRI machine. It was intended to be a It was intended to be a stacked set of axial image acquisitions with ~0.35 mm x ~0.35 mm in plane resolution and 0.7 mm image thickness (no gap).

Sequence name: pd_tse_cor_p2_384 Plane: Axial FOV (mm): 180 x 75% --> 180 x 135 x 135 Slice thickness/gap (mm/mm): 0.7/0 TR (ms): 1390 TE (ms): 14 # of slices: 36 (x 7) Flip angle (deg.): 90 Bandwidth (Hz/pixel): 222 Chemical Shift (pixels): No. excitations averaged: 1 ETL: 14 Phase encode axis: Distance factor (%): 0 Phase oversampling: Slice oversampling: 0 Phase/slice/read resolution: Slice partial Fourier: Phase partial Fourier: Readout partial Fourier: X-resolution (mm): 180/512 --> 0.3516 Scan time (min.): ~23 min

Discussion

-- ["aerdemir"] DateTime(2014-03-10T12:26:15Z) Based on the results above, should our specimen imaging trial include

1. T1-ISO WITHOUT FAT SUPPRESSION: (0.5 mm x 0.5 mm x 0.5 mm) for overall imaging of the knee including registration markers.
2. T1 VIBE (DESS-LIKE CONTRAST AND RESOLUTION): (0.341 mm x 0.341 mm x 0.7 mm slice thickness no gap: sagittal plane) for reconstruction of bone and cartilage. This may be helpful to reconstruct cruciate ligaments and menisci.
3. MESE-TYPE TSE 2D: (0.341 mm x 0.341 mm x 2 mm slice thickness no gap (or 1mm slice thickness with 2 mm gap) - multi plane: sagittal, coronal, and axial) for reconstruction of ligaments, tendons, and menisci. We may need to run another test trial to see if we can acquire such scans with a desirable FOV and contrast.

Imaging Trial 3: February 17, 2014

Attendees: Chris, Shannon (UH); Ahmet, Craig, Snehal (CC)

The goal of this imaging trial was to conduct a full mock-up imaging of a knee specimen including:

• an isotropic T1 weighted imaging (based on CoBi Core's previous protocols),

• a sagittal plane DESS imaging (based on OAI protocols), and
• an axial plane MESE imaging (based on OAI protocols).

In addition, alignment of the image sets in the MR coordinate system was elaborated upon.

Remarks during Session (Ahmet)

• The center image location will be provided. This information may not be correct in DICOM files.
• Support to fill-in the settings table, as in OAI manuscript, need to be provided.
• Oblique imaging will be conducted so that image sets become orthogonal.
• Sequence name and settings will be provided.
• Attempted imaging
  • T1; 0.4 mm x 0.4 mm x 0.4 mm (resolution); 230 mm x 160 mm x 160 mm (fov)
    • Contrast is anticipated to look like SEQUENCE 1: T1-ISO (see above).
  • DESE (sagittal plane); 0.35 mm x 0.35 mm x 0.7 mm (resolution); 135 mm x 135 mm x 112 mm (fov)

    • Contrast is anticipated to look like [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048821/figure/F4/ this] (Figure 4 of OAI protocols). Also see SEQUENCE 2: DESS-APPROX (see above).

  • MESE (axial plane); 0.30 mm x 0.30 mm x 2.0 mm (resolution); 120 mm x 120 mm x 180 mm (fov); 3 different T2 settings

    • Contrast is anticipated to look like [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048821/figure/F8/ this] (Figure 8 of OAI protocols, note that OAI protocols are sagittal).

    • Thickness and fov are at the bound of the capabilities of the imaging system.
    • Scan times are long, ~36 min.
• For larger knees out of plane resolution may need to be increased to accommodate increased fov requirement. This can also be compensated by additional scan time while trying to keep desirable resolution.
• Images of higher resolution can be filtered. Number of excitations can be increased at the cost of scan time.

Remarks from UH (Shannon)

Image sequences of mock-up trial of February 17, 2014:

1. Fast 3Plane Loc (this is our rough scan to just get an idea of the location of the leg in each plane)
   • voxel size: 2.3*2.3*5.0mm
   • slice thickness: 0.5mm
   • 1 slice, every different plane
2. Arc T1 axial (actually sagittal)
   • voxel size: 1.2*1.2*1.6mm
   • slice thickness: 1.6mm
   • 50 slices
3. t1_F13d_sag_P2_iso_0.4_we
   • voxel size: 0.4 * 0.4 * 0.4mm
   • slice thickness: 0.40mm
   • position: L5.1, A 37.0, H10.2
   • 320 slices/slab (1 slab)
4. dess_3dsag_we
   • voxel size: 0.4*0.4*0.7mm
   • slice thickness: 0.70mm
   • position: L5.1, A34.8, H21.3
   • 160 slices/slab (1 slab)
5. tse_te20-40-60_300um (this is your MSME)
   • voxel size: 0.3*0.3*2mm
   • slice thickness: 2mm
   • position: L1.5, A38.5, H11.5
   • 90 slices

Results

T1-ISO:

attachment:T1_iso_HEADER.txt

Axial:

attachment:T1_iso_axl_02.17.14.png

Sagittal:

attachment:T1_iso_sagl_02.17.14.png

Coronal:

attachment:T1_iso_cor_02.17.14.png

DESS:

attachment:DESS_iso_HEADER.txt

attachment:DESS_sag_02.17.14.png

MESE:

attachment:MESE_iso_HEADER.txt

attachment:MESE_axl_02.17.14.png

Imaging Trial 2: January 29, 2014

Imaging Trial 1: November 14, 2013

-- ["hallorj"] DateTime(2013-11-05T15:11:02Z) An imaging test session is setup for November 14, 2013 from 1-2:30 pm. Myself and/or Snehal will attend. The BioRobotics Core can provide a knee specimen. If the specimen is currently a whole leg, we'll need to prepare it for imaging. Thawing will have to occur the day before. During the test session, we will look at the metal artifact issue (bring the brass mounting plugs) and image acquisition settings will be tested. I envision starting from the T1 weighted settings we currently use and adding one of the above T2 acquisitions. The T2 set should focus on cartilage while the T1 should be good for the other soft-tissues (ligaments, tendon, meniscus). An email will be sent to Dr. Carl Winalski (a radiologist and member of the advisory board) for feedback on the settings.

Results from imaging testing session conducted on November 14, 2013.

Machine: Siemens MAGNETOM Skyra 3T, Clinical

Receiver Coil: knee coil

Sequence 1:

• T2 proton density.
• DICOM header: attachment:t2_protondensity.txt

attachment:cor_t2_iso.png

Sequence 2: DESS-APPROX

• 3D dual-echo in steady state (DESS), first approximation of OAI DESS protocol

  • Reference: http://www.ncbi.nlm.nih.gov/pubmed/18786841

• DICOM header: attachment:DESS_approx_sag_HEADER.txt

attachment:cor_3dDESS.png attachment:sag_3dDESS.png

• Coronal and sagittal image samples showing articular cartilage and PCL respectively

Sequence 3: BRASS ARTIFACTS

• Evaluation of image artefacts caused by brass components of marker fixture.
  • Marker components and a piece of delrin were taped to a piece of paper and placed on the MRI phantom.
  • Bottom right shadow in the image below is resulted from a piece of delrin. Rest of the artefacts are due to brass components.

attachment:phantoms.png

Hargreaves, Brian A, Pauline W Worters, Kim Butts Pauly, John M Pauly, Kevin M Koch, and Garry E Gold. “Metal-induced artifacts in MRI.” AJR. American journal of roentgenology 197, no. 3 (September 2011): 547–555. doi:10.2214/AJR.11.7364. http://www.ncbi.nlm.nih.gov/pubmed/21862795

-- ["aerdemir"] DateTime(2014-02-24T12:19:34Z) For each imaging sequence, provide a sample image and the DICOM header as a text file.