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See https://github.com/rg2/DeepFluoroLabeling-IPCAI2020 for complete details on obtaining the dataset and HDF5 file layouts.
The full resolution, non-preprocessed, dataset (ipcai_2020_full_res_data.h5) is used by these tools and is available here.
The CT volume, CT volume segmentation, and 3D anatomical landmarks may be extracted using the xreg-ipcai-extract-3d-data tool.
The specimen ID string is used to select which 3D data to extract.
For example, the following command will extract the 3D data for specimen 1:
xreg-ipcai-extract-3d-data ipcai_2020_full_res_data.h5 17-1882 spec_1_vol.nii.gz spec_1_vol_seg.nii.gz spec_1_3d_lands.fcsv
Examination of the extracted volumes and landmarks may conducted using 3D Slicer as shown by the screenshot below:
2D projections are extracted using the xreg-ipcai-extract-proj-data tool.
As shown by the command below, the specimen ID and projection index are used to select the 2D data to extract:
xreg-ipcai-extract-proj-data ipcai_2020_full_res_data.h5 17-1882 96 proj_96.h5
The projection may be previewed using the xreg-remap-tile-proj-data tool, with the following command creating the projection preview below:
xreg-remap-tile-proj-data proj_96.h5 proj_96_01.png -d 0.25
The xreg-ipcai-global-pelvis-regi tool will attempt to register the pelvis to projection 96 without any 2D annotations or manually adjusted initialization.
The first positional argument must be either 1 or 2 and is used to specify the global registration strategy.
See the IPCAI/IJCARS paper for the details of each approach.
A registration using method is run using the following command:
xreg-ipcai-global-pelvis-regi -v 1 spec_1_vol.nii.gz spec_1_vol_seg.nii.gz spec_1_3d_lands.fcsv proj_96.h5 proj_96_global_pelvis_method_1_regi.h5 proj_96_global_pelvis_method_1_debug.h5
The registration may be verified using the xreg-regi2d3d-replay tool as demonstrated by the following command:
xreg-regi2d3d-replay proj_96_global_pelvis_method_1_debug.h5 --proj-ds 0.5 --video-fps 10
This should create two movies (edges.mp4 and mov.mp4) similar to the below animations:
The edge overlay demonstrates that the pelvis registration is sufficient for further refinement and additional femur registration. Had the registration been insufficient, the second method could be invoked and replay movies created with the following commands:
xreg-ipcai-global-pelvis-regi -v 2 spec_1_vol.nii.gz spec_1_vol_seg.nii.gz spec_1_3d_lands.fcsv proj_96.h5 proj_96_global_pelvis_method_2_regi.h5 proj_96_global_pelvis_method_2_debug.h5
xreg-regi2d3d-replay proj_96_global_pelvis_method_2_debug.h5 --proj-ds 0.5 --video-fps 10
The replay tool should produce animations similar to those below, which indicate X:
TODO