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PHANTOM-FDA

Phantom FDA | Phantom FDA

DOI: 10.7937/k9/TCIA.2015.orbjkmux | Data Citation Required | Image Collection

Location Species Subjects Data Types Cancer Types Size Status Updated
Lung Phantom Human 7 CT Phantom 782.22GB Public, Complete 2017/08/30

Summary

As part of a more general effort to probe the interrelated factors impacting the accuracy and precision of lung nodule size estimation, we have been conducting phantom CT studies with an anthropomorphic thoracic phantom containing a vasculature insert on which synthetic nodules were inserted or attached.

The utilization of synthetic nodules with known truth regarding size and location allows for bias and variance analysis, enabled by the acquisition of repeat CT scans.  Using a factorial approach to probe imaging parameters (acquisition and reconstruction) and nodule characteristics (size, density, shape, location), ten repeat scans have been collected for each protocol and nodule layout.  The resulting database of CT scans is incrementally becoming available to the public via The Cancer Imaging Archive (TCIA) to facilitate the assessment of lung nodule size estimation methodologies and the development of image analysis software among other possible applications. 

Data Access

Version 2: Updated 2017/08/30

Title Data Type Format Access Points Subjects Studies Series Images License
Images CT DICOM
Download requires NBIA Data Retriever
7 76 4,433 1,468,751 CC BY 3.0
DICOM Metadata Digest CSV CC BY 3.0

Additional Resources for this Dataset

The NCI Cancer Research Data Commons (CRDC) provides access to additional data and a cloud-based data science infrastructure that connects data sets with analytics tools to allow users to share, integrate, analyze, and visualize cancer research data.

  • Imaging Data Commons (IDC) (Imaging Data)
  • Citations & Data Usage Policy

    Data Citation Required: Users must abide by the TCIA Data Usage Policy and Restrictions. Attribution must include the following citation, including the Digital Object Identifier:

    Data Citation

    Gavrielides, M. A., Kinnard, L. M., Myers, K. J., Peregoy, J., Pritchard, W. F., Zeng, R., Esparza, J., Karanian, J., & Petrick, N. (2015). Data From Phantom FDA [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/k9/TCIA.2015.orbjkmux

    Detailed Description

    Database Description (link)

    The anthropomorphic thoracic phantom (Kyotokagaku Incorporated, Tokyo, Japan) employed in this study is shown in Figure 1, along with the vasculature insert on which synthetic nodules were attached before CT imaging.  The phantom does not contain lung parenchyma so the space within the vascular structure is filled with air.

    fig1.PNG

    Fig 1:  Photograph of the exterior shell of the thoracic phantom (left) and the vasculature insert (right).

    The synthetic lung nodules used in our data CT scans were manufactured by either Kyotokagaku Incorporated (Japan) and Computerized Imaging Reference Systems (CIRS, Norfolk, VA).  They consisted of objects varying in size (5, 8, 10, 12, 20, 40 mm), shape (spherical, elliptical, lobulated, spiculated), and density (-800, -630, -10, +100 HU).  Figure 2 shows examples of the various sizes and shapes of synthetic nodules used in our CT data collection.

    Eight different layouts of nodules were specified by placing them in premarked positions within the phantom vasculature, where they were either attached to vessels or suspended in foam (non-attached configuration).  Care was taken to maintain constant positioning of the nodules when a particular layout was scanned multiple times or with different protocols.  For that purpose, vessels on which nodules were attached were color coded.  Table 1 tabulates the nodule configuration for the nodule layouts that are currently available at NBIA DICOM Radiology Portal in terms of nodule positioning, size, shape, and density. Figures 3-6 show a schematic diagram of the currently available layouts.  All tables and figures in this document will be updated as more data is posted.

     

    Figure 2:  Photographs of the different types of synthetic nodules used in this study.  Each column shows example nodules in three sizes, with lobulatedellipticalspiculatedspherical, and irregular nodules shown from left to right.  The three sizes shown here were manufactured to have the equivalent volumes of spherical nodules with diameters of 5, 10, and 20 mm (with the exception of the irregular shapes which have nominal diameters of about 5, 10, 12 mm).  Additional nodules used in this study span the size range between 5-60mm.

     

    Nodule layout

    Vessel attachment

    Nodule placement and description

    Left lung

    Right lung

    Nominal diameter (mm)

    Shape*

     

    HU

    Nominal diameter (mm)

    Shape

    HU

    1

    attached

    5,8,10

    SPH   

    -800

    5,8,10

    SPH

    -630

    2

    attached

    5,8,10

    SPH

    100

    8,12,15

    irregular

    -300, 30,30

    3

    attached

    5,8,10,20,40

    SPH

    100

    5,8,10,20,40

    SPH

    -630

    4

    attached

     10, 20, 10, 20,

    10, 20

    ELL,  ELL,  LOB, LOB, SPI, SPI

     -630

    10, 20, 10, 20,

    10, 20

    ELL^,  ELL, LOB, LOB, SPI, SPI

    100

     Table 1.  Summary of currently available nodule layouts.  *SPH- spherical, ELL- elliptical, LOB- lobulated, SPI- spiculated.  ^Note: The 10mm, 100HU elliptical nodule in the right lung has a large hole in it.  A replacement was scanned as part of Nodule 6 which will be released by the end of 2014.

    The phantom was scanned using a Philips 16-row scanner (Mx8000 IDT, Philips Healthcare, Andover, MA) and a Siemens 64-row scanner (Somatom Definition 64, Siemens Medical Solutions USA, Inc., Malvern, PA).  Scans were acquired with varying combinations of effective dose, pitch, and slice collimation, and were reconstructed with varying combinations of slice thicknesses and reconstruction kernels.  Ten exposures were acquired for each imaging protocol.  The phantom position was not changed during the 10 repeat exposures; however it was repositioned between different imaging protocols or different nodule layouts.  Table 2 summarizes the imaging protocols for the nodule layout.

    NOTE:  Each study in the database contains 10 repeat scans for that particular acquisition protocol, multiplied by the number of reconstructions.   The study and series descriptions contain the following information:

    Study description

    Contains information on: the scanner vendor (currently Philips or Siemens), the exposure (in mAs), the pitch (currently either 1.2 or 0.9 according to the definition  , where Δd is the patient table travel in the horizontal direction and T is the detector width at the isocenter plane),  and slice collimation (in mm).

    Series description:

      Contains information on reconstructed slice thickness (in mm), reconstructed slice increment (in mm), and reconstruction filter or kernel (currently either C for detail, or B for medium).

    Nodule

    Layout, Scanner

    Eff.dose

    (mAs)

    Slice collimation (mm)

    Slice overlap

    Pitch

    Recon. Slice thickness (mm)

    Recon. Kernels

    # sets

    1,S1

    20,50,100,200

    16×0.75,

    (16×1.5)

    50%

    0.9,1.2

    0.75,1.5,3 (2,3,5)

    C

    480

    2, S1

    20,100,200

    16×0.75,

    (16×1.5)

    50%

    0.9,1.2

    0.75,1.5,3 (2,3,5)

    C, B

    720

    3, S2

    25, 100, 200

    64×0.6

    0%, 50%

    0.9, 1.2

    0.75, 1.5, 3.0

    B40f, B60f

    720

    4, S1

    25, 100, 200

    16×0.75,

    (16×1.5)

    50%

    0.9,1.2

    0.75,1.5,3 (2,3,5)

    C, B

    720

    TOTAL

    2640

    Table 2.  Summary of reconstructed CT datasets: a description of the individual nodule layouts are provided in Table 3. *S1: 16-row Philips Mx8000 IDT (Philips Healthcare, Andover, MA), S2: 64-row Siemens Somatom (Siemens, Erlangen, Germany).

    For example: there are 16 studies for Nodule Layout #1 (4 exposures x 2 slice collimations x 2 pitch settings).  Each study contains 30 series (10 repeat scans x 3 reconstructed slice thickness x 1 reconstruction kernel).

    A key component of the CT lung phantom project is the ability to compare the estimated nodule size with the known true size or reference gold standard.  As part of our project, volume was used as a surrogate measure of size.   The true volume estimate of each synthetic nodule was derived from weight and density measures.  Both the CIRS-and Kyotokagaku nodules were accompanied by density measures.  Nodule weights were measured in our lab using a precision scale of 0.1 mg tolerance (Adventurer Pro AV 2646, Ohaus Corp, Pine Brook, NJ).  Three repeat weight measurements were made and these weights were averaged to produce a final estimated weight for each nodule.  Our estimates of the true volume of the synthetic nodules in each layout are summarized in Table 3 along with approximated xyz location (based on 0.8mm slice thickness) of nodule center in the CT scans. 

    This phantom and the associated synthetic nodules designed in our lab have been used in a number of studies examining the accuracy and precision of volumetric measurements using CT

    Nodule

    Layout

    Right lung nodules

    Left lung nodules

    Nom.  Diam.(mm)

    Shape

    HU

    x y z

    Vol

    (µl)

    Nom.  Diam.

    (mm)

    Shape

    HU

    x y z

    Vol (µl)

    1

    5

    SPH

    -630

    177 342 192

    71

    5

    SPH

    -800

    340 325 168

    62

    8

    SPH

    -630

    179 288 531

    282

    8

    SPH

    -800

    343 274 540

    245

    10

    SPH

    -630

    170 309 385

    522

    10

    SPH

    -800

    394 260 363

    496

    2

    8

    irr

    -300

    184 290 525

    253

    5

    SPH

    100

    335 331 157

    64

    12

    irr

    30

    170 319 379

    676

    8

    SPH

    100

    351 282 538

    255

    15

    irr

    30

    189 347 161

    263

    10

    SPH

    100

    395 276 349

    506

    3

    5

    SPH

    -630

    192 350 562

    71

    5

    SPH

    100

    338 328 580

    64

    8

    SPH

    -630

    185 287 208

    282

    8

    SPH

    100

    355 278 212

    255

    10

    SPH

    -630

    170 324 354

    522

    10

    SPH

    100

    394 270 390

    506

    20

    SPH

    -630

    157 251 190

    4193

    20

    SPH

    100

    384 240 229

    4215

    40

    SPH

    -630

    168 280 198

    34524

    40

    SPH

    100

    373 262 156

    33781

    4

    10

    ELL

    -630

    176 354 178

    547

    10

    ELL

    100

    341 333 162

    545

    20

    ELL

    -630

    169 322 95

    4210

    20

    ELL

    100

    401 296 122

    4155

    10

    LOB

    -630

    159 329 347

    530

    10

    LOB

    100

    395 272 329

    535

    20

    LOB

    -630

    136 292 337

    4305

    20

    LOB

    100

    349 350 268

    4441

    10

    SPI

    -630

    167 315 520

    539

    10

    SPI

    100

    357 296 530

    535

    20

    SPI

    -630

    133 269 475

    4335

    20

    SPI

    100

    386 248 503

    4305

    Table 3.  Approximate center location and estimated true volume of synthetic lung nodules in each nodule layout based on 0.75mm slice thickness, 0.4mm slice increment CT scans.  (SPH=spherical, ELL=elliptical, LOB= lobulated, SPI= spiculated, irr=irregular)

      

    Please contact help@cancerimagingarchive.net who can direct you to Dr. Gavrielides with further scientific questions.


    Appendix 1

     layout1.PNG

     Figure 3.  Schematic diagram of Nodule Layout#1 in terms of nodule placement. Vessel branches within the anthropomorphic phantom were color coded for the purpose of mapping nodules to specific positions within the phantom’s vasculature structure in a reproducible manner.

    layout2.PNG 

    Figure 4.  Schematic diagram of Nodule Layout#2 in terms of nodule placement.

    Figure 5.  Schematic diagram of Nodule Layout#3 in terms of nodule placement.

    Figure 6.  Schematic diagram of Nodule Layout#4 in terms of nodule placement.

    Other Publications Using this Data

    TCIA maintains a list of publications which leverage our data.  If you have a manuscript you’d like to add please contact TCIA’s Helpdesk.

    1. Kalpathy-Cramer, J., et al, (2016) “Radiomics of Lung Nodules: A Multi-Institutional Study of Robustness and Agreement of Quantitative Imaging Features.” Tomography 2(4)430-437. doi:  10.18383/j.tom.2016.00235
    2. Peskin AP, Dima AA, Saiprasad G. An Automated Method for Locating Phantom modules in Anthropomorphic Thoracic Phantom CT Studies. The 2012 International Conference on Image Processing, Computer Vision, and Pattern Recognition. 2012. (IPC conference link)

    Publication Citation

    Gavrielides, M. A., Kinnard, L. M., Myers, K. J., Peregoy, J., Pritchard, W. F., Zeng, R., Esparza, J., Karanian, J., & Petrick, N. (2010). A resource for the assessment of lung nodule size estimation methods: database of thoracic CT scans of an anthropomorphic phantom. In Optics Express (Vol. 18, Issue 14, p. 15244).  https://doi.org/10.1364/oe.18.015244,  PMCID: PMC3408907

    TCIA Citation

    Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., & Prior, F. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. In Journal of Digital Imaging (Vol. 26, Issue 6, pp. 1045–1057). Springer Science and Business Media LLC. https://doi.org/10.1007/s10278-013-9622-7

    Previous Versions

    Version 1: Updated 2014/08/04

    Title Data Type Format Access Points Studies Series Images License
    Images DICOM
    DICOM Metadata Digest CSV