Overview | Export the ROIs from 'OsiriX' | Example data | ROI voxels | Radiomics features with 'PyRadiomics'
Package: osirad 0.1.0
Tao Lan
osirad: PET Voxels and Radiomics from 'OsiriX' Regions of Interest
Reads regions of interest (ROIs) drawn in the 'OsiriX' medical image viewer and exported as XML files, and recovers the exact voxels of each ROI on the positron emission tomography (PET) series stored as Digital Imaging and Communications in Medicine (DICOM) files. The voxels are found by matching the voxel values stored in the XML file to the standardised uptake values (SUV) computed from the DICOM header. The resulting voxel table (positions in pixels and millimetres, and SUV) can be passed to the 'Python' library 'PyRadiomics' (van Griethuysen et al. (2017) <doi:10.1158/0008-5472.CAN-17-0339>) through 'reticulate' to compute radiomics features.
Authors:
osirad_0.1.0.tar.gz
osirad_0.1.0.zip(r-4.7-any)osirad_0.1.0.zip(r-4.6-any)
osirad_0.1.0.tar.gz(r-4.7-any)osirad_0.1.0.tar.gz(r-4.6-any)
osirad_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
osirad/json (API)
| # Install 'osirad' in R: |
| install.packages('osirad', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tao-lan/osirad/issues
Last updated from:ed819f3dbd. Checks:6 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 117 | ||
| source / vignettes | OK | 194 | ||
| linux-release | OK | 110 | ||
| windows-devel | OK | 68 | ||
| windows-release | OK | 69 | ||
| wasm-release | OK | 98 |
Exports:extract_roi_voxelsmatch_roi_voxelsplot_roi_slicespyradiomics_featuresread_osirix_roisread_pet_slicesuv_factor_from_header
Dependencies:abindbitopsclioro.dicomoro.niftiRcpprlangRNiftixml2
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Extract the voxels of 'OsiriX' ROIs from a PET DICOM series | extract_roi_voxels |
| Find the voxels of one ROI on one PET slice | match_roi_voxels |
| Plot PET slices with the ROI voxels | plot_roi_slices |
| Radiomics features of the ROI voxels with 'PyRadiomics' | pyradiomics_features |
| Read regions of interest exported from 'OsiriX' | read_osirix_rois |
| Read one PET slice in SUV | read_pet_slice |
| SUV factor from a PET DICOM header | suv_factor_from_header |