Walkthrough Files

A list of download links for the files created as a result of following the walkthrough is shown below. The files are listed in an order that approximately follows the walkthrough steps. Some of these files may differ from the files created independently on your machine due to various factors, such as random sampling used to create the data, changes in the software, and platform differences.

• lymph.nii.gz
  • Created in DICOM conversion and resampling
  • Used in DICOM conversion and resampling, volume cropping
• head.nii.gz
  • Created and used in DICOM conversion and resampling
• 0522c0012_00.nii.gz
  • Created in DICOM conversion and resampling
• ABD_LYMPH_001_00.nii.gz
  • Created in DICOM conversion and resampling
• Pelvic-Ref-007_00.nii.gz
  • Created in DICOM conversion and resampling
  • Used in DICOM conversion and resampling, simulated fluoroscopy
• 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, PAO planning and fragment creation, PAO volumetric modeling, point cloud to surface registration, single-view pelvis registration, multi-view/multi-object registration
• pelvis_seg.nii.gz: Bone segmentation of pelvis.nii.gz.
  • Created in bone segmentation
  • Used in mesh creation, PAO planning and fragment creation, screw and K-wire volumetric modeling, single-view pelvis registration, multi-view/multi-object registration
• 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
  • Used in point cloud to surface registration, single-view pelvis registration
• 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
  • Created in PAO planning and fragment creation
  • Used in PAO planning and fragment creation, PAO random adjustment, PAO volumetric modeling, screw and K-wire volumetric modeling, simulated fluoroscopy, multi-view/multi-object registration
• 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
  • Created and used in PAO planning and fragment creation
• pao_cut_defs.h5
  • Created and used in PAO planning and fragment creation
• pao_cuts_seg.nii.gz
  • Created in PAO planning and fragment creation
  • Used in PAO planning and fragment creation, PAO random adjustment, PAO volumetric modeling, screw and K-wire volumetric modeling, multi-view/multi-object registration
• pao_cut_defs_batch_000.h5
  • Created and used in PAO planning and fragment creation
• pao_cuts_seg_batch_000.nii.gz
  • Created and used in PAO planning and fragment creation
• test_pao_frag_0.h5
  • Created in PAO random adjustment
  • Used in PAO random adjustment, PAO volumetric modeling, screw and K-wire volumetric modeling
• test_pao_femur_0.h5
  • Created in PAO random adjustment
  • Used in PAO random adjustment, PAO volumetric modeling, screw and K-wire volumetric modeling
• pao_vol.nii.gz
  • Created in PAO volumetric modeling
  • Used in screw and K-wire volumetric modeling
• pelvis_left_insertion_labels.nii.gz
  • Created and used in in screw and K-wire volumetric modeling
• pao_vol_with_kwire.nii.gz
  • Created in screw and K-wire volumetric modeling
  • Used in simulated fluoroscopy
• pao_vol_with_screws.nii.gz
  • Created in screw and K-wire volumetric modeling
• example1_1_pd_003.h5
  • Created in simulated fluoroscopy
  • Used in simulated fluoroscopy, single-view pelvis registration, multi-view/multi-object registration
• example1_1_pose_003.h5
  • Created and used in simulated fluoroscopy
• pao_w_kwire_mesh.h5
  • Created and used in simulated fluoroscopy
• example1_2_pd_003.h5
  • Created and used in simulated fluoroscopy
• example1_2_pose_003.h5
  • Created and used in simulated fluoroscopy
• example1_3_pd_000.h5
  • Created and used in simulated fluoroscopy
• Pelvic-Ref-007_00_app_lands.fcsv
  • Created and used in simulated fluoroscopy
• example2_pd_000.h5
  • Created and used in simulated fluoroscopy
• pelvis_preop_lands.fcsv
  • Created and used in point cloud to surface registration
• pelvis_intraop_lands.fcsv
  • Created and used in point cloud to surface registration
• pelvis_intraop_point_cloud.fcsv
  • Created and used in point cloud to surface registration
• pelvis_regi.h5
  • Created and used in point cloud to surface registration
• pelvis_intraop_point_cloud_regi.fcsv
  • Created and used in point cloud to surface registration
• pelvis_regi_2d_3d_lands.fcsv
  • Created and used in single-view pelvis registration
• example1_1_pd_003_proj_000.nii.gz
  • Created and used in single-view pelvis registration
• example1_1_pd_003_proj_0_lands.fcsv
  • Created and used in single-view pelvis registration
• example1_1_pd_003.h5 (after inserting landmarks from example1_1_pd_003_proj_0_lands.fcsv)
  • Created in single-view pelvis registration
  • Used in single-view pelvis registration, multi-view/multi-object registration

References

• All of the non-derived data in the walkthrough was obtained from The Cancer Imaging Archive (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)
• The lymph.nii.gz and ABD_LYMPH_001_00.nii.gz volumes were created using the TCIA "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)
• The head.nii.gz and 0522c0012_00.nii.gz volumes were created using the TCIA "Head-Neck Cetuximab" dataset:
  • 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
• The Pelvic-Ref-007_00.nii.gz volume was created using the TCIA "Pelvic Reference" dataset:
  • 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).