Walkthrough: Data

Walkthrough Files

• lymph.nii.gz
• R.acsv: Region of interest (ROI) file for the pelvis in lymph.nii.gz
  • Created and used in volume cropping
• pelvis.nii.gz: Cropped version of lymph.nii.gz about the pelvis using R.acsv.
  • Created in volume cropping
  • Used in bone segmentation, mesh creation
• pelvis_seg.nii.gz: Bone segmentation of pelvis.nii.gz.
  • Created in bone segmentation
  • Used in mesh creation, pao planning and fragment creation
• pelvis_thresh_sur.ply: Surface mesh created from basic HU thresholding
  • Created in mesh creation
• pelvis_sur.ply: Surface mesh of the pelvis created using pelvis_seg.nii.gz
  • Created in mesh creation
• pelvis_app_lands.fcsv: Landmarks used to define the anterior pelvic plane (APP) of the pelvis in lymph.nii.gz, pelvis.nii.gz, pelvis_seg.nii.gz
• pao_cut_lands.fcsv: Landmarks used to define bilateral PAO plans for the pelvis in lymph.nii.gz, pelvis.nii.gz, pelvis_seg.nii.gz
• pao_cut_defs.h5
• pao_cuts_seg.nii.gz
• pao_cut_defs_batch_000.h5
• pao_cuts_seg_batch_000.nii.gz
• test_pao_frag_0.h5
• test_pao_femur_0.h5
• pao_vol.nii.gz
• pelvis_left_insertion_labels.nii.gz
• pao_vol_with_kwire.nii.gz
• pao_vol_with_screws.nii.gz

References

• TCIA
  • Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. (link)
• Lymph Nodes Dataset
  • Holger, Roth, Lu, Le, Seff, Ari, Cherry, Kevin M, Hoffman, Joanne, Wang, Shijun, … Summers, Ronald M. (2015). A new 2.5 D representation for lymph node detection in CT. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2015.AQIIDCNM
  • Roth, Holger R and Lu, Le and Seff, Ari and Cherry, Kevin M and Hoffman, Joanne and Wang, Shijun and Liu, Jiamin and Turkbey, Evrim and Summers, Ronald M. A new 2.5 D representation for lymph node detection using random sets of deep convolutional neural network observations. Medical Image Computing and Computer-Assisted Intervention--MICCAI 2014, p520-527, 2014. (link)
  • Seff, Ari and Lu, Le and Cherry, Kevin M and Roth, Holger R and Liu, Jiamin and Wang, Shijun and Hoffman, Joanne and Turkbey, Evrim B and Summers, Ronald M. 2D view aggregation for lymph node detection using a shallow hierarchy of linear classifiers. Medical Image Computing and Computer-Assisted Intervention--MICCAI 2014, p544-552, 2014. (link)
• Head-Neck Cetuximab
  • Bosch, Walter R., Straube, William L., Matthews, John W., & Purdy, James A. (2015). Data From Head-Neck_Cetuximab. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2015.7AKGJUPZ
• Pelvic Reference Data
  • Afua A. Yorke, Gary C. McDonald, David Solis Jr., Thomas Guerrero. (2019) Pelvic Reference Data. The Cancer Imaging Archive. DOI: 10.7937/TCIA.2019.woskq5oo
  • Yorke A, McDonald GC, Solis Jr. D, Guerrero T. A Statistically Characterized Reference Data Set for Image Registration of Pelvis Using Combinatorial Rigid Registration Registration Optimization (CORRO).