{ "_id": "6aea263d9ceaa78f2009decf", "Package": "scimagR", "Title": "Spinal Cord Injury Imaging Pipeline for MRI and CT Analysis in R", "Version": "0.1.0", "Authors@R": "person(\"R.\", \"Heller\", role = c(\"aut\", \"cre\"),\nemail = \"raban.heller@example.com\")", "Description": "An end-to-end pipeline for longitudinal MRI and CT\nanalysis in spinal cord injury (SCI) research. Provides R\nwrappers for the Spinal Cord Toolbox (SCT) including SCIsegV2\nlesion segmentation, DICOM anonymization and NIfTI conversion\ntools, SCI-specific clinical metrics (MSCC, compression ratio,\ntissue bridge quantification), implant artifact grading, and\npipeline orchestration with built-in quality control.\nIntegrates with workflowr for reproducible, publication-ready\nneuroimaging analyses.", "License": "MIT + file LICENSE", "URL": "https://github.com/cttir/scimagR", "BugReports": "https://github.com/cttir/scimagR/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "SystemRequirements": "Spinal Cord Toolbox (>= 6.4)\n, dcm2niix\n, Python 3 with pydicom\n(pip install pydicom)", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/Needs/website": "CTTIR/themakR", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libicu-dev python3 libx11-dev zlib1g-dev", "Repository": "https://cttir.r-universe.dev", "Date/Publication": "2026-10-28 07:29:17 UTC", "RemoteUrl": "https://github.com/CTTIR/scimagR", "RemoteRef": "HEAD", "RemoteSha": "7cbb2555d64b81592b23a2eba787702721bc65d0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-03 18:18:09 UTC", "User": "root" }, "Author": "R. Heller [aut, cre]", "Maintainer": "R. Heller ", "_user": "cttir", "_type": "src", "_file": "scimagR_0.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/1ee3fe7926200daff91a92fce6ff9d5dcc2ecad3906b86736384041a9a8fd920", "_filesize": 1071139, "_sha256": "1ee3fe7926200daff91a92fce6ff9d5dcc2ecad3906b86736384041a9a8fd920", "_expires": "2027-02-11T18:21:47.000Z", "_created": "2026-11-03T18:18:09.000Z", "_published": "2026-11-03T18:21:49.747Z", "_upstream": "https://github.com/CTTIR/scimagR", "_status": "success", "_maintainer": { "name": "R. Heller", "email": "raban.heller@example.com" }, "_jobs": [ { "job": 126114529247, "time": 134, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13258121095" }, { "job": 126114529270, "time": 176, "config": "linux-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13257931545" }, { "job": 126114529143, "time": 98, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "13256969360" }, { "job": 126114529027, "time": 122, "config": "macos-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13256499685" }, { "job": 126112425353, "time": 221, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13257203833" }, { "job": 126114529073, "time": 120, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13256164885" }, { "job": 126114529297, "time": 89, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13258340377" }, { "job": 126114529663, "time": 112, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13256519510" }, { "job": 126114529265, "time": 95, "config": "windows-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13256469645" } ], "_buildurl": "https://github.com/r-universe/cttir/actions/runs/41691849296", "_commit": { "id": "7cbb2555d64b81592b23a2eba787702721bc65d0", "author": "R. Heller <58561665+r-heller@users.noreply.github.com>", "committer": "R. Heller <58561665+r-heller@users.noreply.github.com>", "message": "Update named v5 package branding\n", "time": 1793172557 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "cli", "version": ">= 3.0", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.1", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.4", "role": "Imports" }, { "package": "glue", "version": ">= 1.6", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "rlang", "version": ">= 1.0", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "viridisLite", "role": "Imports" }, { "package": "writexl", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "here", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "rstudioapi", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "workflowr", "role": "Suggests" } ], "_owner": "cttir", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-19", "n": 1 }, { "week": "2026-24", "n": 5 }, { "week": "2026-25", "n": 1 }, { "week": "2026-26", "n": 2 }, { "week": "2026-33", "n": 1 }, { "week": "2026-34", "n": 2 }, { "week": "2026-42", "n": 4 }, { "week": "2026-43", "n": 3 }, { "week": "2026-44", "n": 4 } ], "_tags": [ { "name": "v0.1.0", "date": "2026-05-04" } ], "_stars": 0, "_contributors": [ { "user": "r-heller", "count": 24, "uuid": 58561665 } ], "_userbio": { "uuid": 275040041, "type": "organization", "name": "CTTIR", "followers": 10, "description": "Computational Trauma and Tissue Injury Research" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/scimagR" }, "_devurl": "https://github.com/cttir/scimagr", "_searchresults": 6, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/scimagR.html", "LICENSE" ], "_cranurl": false, "_exports": [ "anonymize_dicom", "check_dcm2niix", "check_pydicom", "check_sct", "classify_artifact", "classify_phase", "compute_compression_ratio", "compute_csa_ratio", "compute_mscc", "convert_batch", "convert_dcm2niix", "coverage_matrix", "create_qc_log", "create_registry", "extract_dicom_metadata", "filter_evaluable", "integrity_summary", "log_exclusion", "pal_artifact", "pal_modality", "pal_phase", "plot_coverage", "plot_forest", "plot_spaghetti", "plot_violin_box", "save_fig", "save_rds", "save_table", "scale_colour_artifact", "scale_colour_modality", "scale_colour_phase", "scale_fill_artifact", "scale_fill_modality", "scale_fill_phase", "sci_create_project", "sci_pipeline_status", "sci_run_pipeline", "sct_analyze_lesion", "sct_generate_qc", "sct_label_vertebrae", "sct_process_segmentation", "sct_segment_lesion", "sct_segment_sc", "theme_sci", "update_qc_log", "validate_qc_log", "validate_registry" ], "_help": [ { "page": "anonymize_dicom", "title": "Anonymize DICOM Files", "topics": [ "anonymize_dicom" ] }, { "page": "check_dcm2niix", "title": "Check dcm2niix Availability", "topics": [ "check_dcm2niix" ] }, { "page": "check_pydicom", "title": "Check pydicom Availability", "topics": [ "check_pydicom" ] }, { "page": "check_sct", "title": "Check Spinal Cord Toolbox Availability", "topics": [ "check_sct" ] }, { "page": "classify_artifact", "title": "Classify MRI Artifact Grade", "topics": [ "classify_artifact" ] }, { "page": "classify_phase", "title": "Classify SCI Phase Based on Days Post Trauma", "topics": [ "classify_phase" ] }, { "page": "compute_compression_ratio", "title": "Compute Spinal Cord Compression Ratio", "topics": [ "compute_compression_ratio" ] }, { "page": "compute_csa_ratio", "title": "Compute Cross-Sectional Area Ratio", "topics": [ "compute_csa_ratio" ] }, { "page": "compute_mscc", "title": "Compute Maximum Spinal Cord Compression (MSCC)", "topics": [ "compute_mscc" ] }, { "page": "convert_batch", "title": "Batch Convert DICOM to NIfTI", "topics": [ "convert_batch" ] }, { "page": "convert_dcm2niix", "title": "Convert DICOM to NIfTI", "topics": [ "convert_dcm2niix" ] }, { "page": "coverage_matrix", "title": "Create a Modality Coverage Matrix", "topics": [ "coverage_matrix" ] }, { "page": "create_qc_log", "title": "Create a QC Segmentation Log", "topics": [ "create_qc_log" ] }, { "page": "create_registry", "title": "Create an Imaging Registry from DICOM Metadata", "topics": [ "create_registry" ] }, { "page": "extract_dicom_metadata", "title": "Extract DICOM Header Metadata", "topics": [ "extract_dicom_metadata" ] }, { "page": "filter_evaluable", "title": "Filter to Evaluable Imaging Sessions", "topics": [ "filter_evaluable" ] }, { "page": "integrity_summary", "title": "Print Data Integrity Summary", "topics": [ "integrity_summary" ] }, { "page": "log_exclusion", "title": "Log an Exclusion Step", "topics": [ "log_exclusion" ] }, { "page": "pal_artifact", "title": "Artifact Grade Colour Palette", "topics": [ "pal_artifact" ] }, { "page": "pal_modality", "title": "Modality Colour Palette", "topics": [ "pal_modality" ] }, { "page": "pal_phase", "title": "SCI Phase Colour Palette", "topics": [ "pal_phase" ] }, { "page": "plot_coverage", "title": "Plot Modality Coverage Matrix", "topics": [ "plot_coverage" ] }, { "page": "plot_forest", "title": "Forest Plot", "topics": [ "plot_forest" ] }, { "page": "plot_spaghetti", "title": "Spaghetti Plot", "topics": [ "plot_spaghetti" ] }, { "page": "plot_violin_box", "title": "Violin + Box Plot", "topics": [ "plot_violin_box" ] }, { "page": "save_fig", "title": "Save Figure with Standard Conventions", "topics": [ "save_fig" ] }, { "page": "save_rds", "title": "Save R Object as RDS", "topics": [ "save_rds" ] }, { "page": "save_table", "title": "Save Table as Excel", "topics": [ "save_table" ] }, { "page": "scale_artifact", "title": "Colour and Fill Scales for Artifact Grades", "topics": [ "scale_artifact", "scale_colour_artifact", "scale_fill_artifact" ] }, { "page": "scale_modality", "title": "Colour and Fill Scales for Imaging Modalities", "topics": [ "scale_colour_modality", "scale_fill_modality", "scale_modality" ] }, { "page": "scale_phase", "title": "Colour and Fill Scales for SCI Phases", "topics": [ "scale_colour_phase", "scale_fill_phase", "scale_phase" ] }, { "page": "sci_create_project", "title": "Create a New SCI MRI/CT Analysis Project", "topics": [ "sci_create_project" ] }, { "page": "sci_pipeline_status", "title": "Get Pipeline Status", "topics": [ "sci_pipeline_status" ] }, { "page": "sci_run_pipeline", "title": "Run the SCI Analysis Pipeline", "topics": [ "sci_run_pipeline" ] }, { "page": "sct_analyze_lesion", "title": "Extract Lesion Parameters", "topics": [ "sct_analyze_lesion" ] }, { "page": "sct_generate_qc", "title": "Generate SCT Quality Control Report", "topics": [ "sct_generate_qc" ] }, { "page": "sct_label_vertebrae", "title": "Label Vertebral Levels", "topics": [ "sct_label_vertebrae" ] }, { "page": "sct_process_segmentation", "title": "Extract Morphometric Parameters", "topics": [ "sct_process_segmentation" ] }, { "page": "sct_segment_lesion", "title": "Segment SCI Lesion", "topics": [ "sct_segment_lesion" ] }, { "page": "sct_segment_sc", "title": "Segment Spinal Cord", "topics": [ "sct_segment_sc" ] }, { "page": "theme_sci", "title": "SCI Publication Theme", "topics": [ "theme_sci" ] }, { "page": "update_qc_log", "title": "Update a QC Log", "topics": [ "update_qc_log" ] }, { "page": "validate_qc_log", "title": "Validate a QC Log", "topics": [ "validate_qc_log" ] }, { "page": "validate_registry", "title": "Validate an Imaging Registry", "topics": [ "validate_registry" ] } ], "_pkglogo": "https://github.com/CTTIR/scimagR/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/CTTIR/scimagR/raw/HEAD/README.md", "_rundeps": [ "bit", "bit64", "cli", "clipr", "cpp11", "crayon", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "hms", "isoband", "labeling", "lifecycle", "magrittr", "pillar", "pkgconfig", "prettyunits", "progress", "purrr", "R6", "RColorBrewer", "readr", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "viridisLite", "vroom", "withr", "writexl" ], "_vignettes": [ { "source": "getting-started.Rmd", "filename": "getting-started.html", "title": "Getting Started with scimagR", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Prerequisites", "Creating a Project", "Data Organization", "Running the Pipeline", "Computing SCI Metrics", "Visualization" ], "created": "2026-05-04 18:05:57", "modified": "2026-10-28 07:29:17", "commits": 5 }, { "source": "pipeline-walkthrough.Rmd", "filename": "pipeline-walkthrough.html", "title": "Pipeline Walkthrough", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Pipeline Steps", "Running the Full Pipeline", "Running Individual Steps", "The QC Pause", "Checking Pipeline Status", "Artifact Grading Strategy", "Coverage Matrix", "Resuming After Interruption" ], "created": "2026-05-04 18:05:57", "modified": "2026-10-28 07:29:17", "commits": 3 }, { "source": "sct-interface.Rmd", "filename": "sct-interface.html", "title": "SCT Interface", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Configuration", "Spinal Cord Segmentation", "Lesion Segmentation (SCIsegV2)", "Vertebral Labeling", "Parameter Extraction", "QC Reports", "Idempotent Execution", "Troubleshooting" ], "created": "2026-05-04 18:05:57", "modified": "2026-10-28 07:29:17", "commits": 3 } ], "_score": 4.1303337684950066, "_indexed": true, "_nocasepkg": "scimagr", "_universes": [ "cttir" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-11-03T18:20:20.000Z", "distro": "resolute", "commit": "7cbb2555d64b81592b23a2eba787702721bc65d0", "fileid": "https://r2.ropensci.org/4e30fe779bf21945989fac31e9fd65226a375eb9653e4cc1981d478ffa096357", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41691849296" }, { "r": "4.6.2", "os": "linux", "version": "0.1.0", "date": "2026-11-03T18:21:03.000Z", "distro": "resolute", "commit": "7cbb2555d64b81592b23a2eba787702721bc65d0", "fileid": "https://r2.ropensci.org/54f31b99abd926d7629c4cec0adfd840b24a3711742be7e101f92e0a5bc03d0b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41691849296" }, { "r": "4.5.3", "os": "mac", "version": "0.1.0", "date": "2026-11-03T18:19:44.000Z", "commit": "7cbb2555d64b81592b23a2eba787702721bc65d0", "fileid": "https://r2.ropensci.org/9ac6544935213815ddb3b6ee8e9757b3de3081075a67624fcd5300d0c1cd85a0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41691849296" }, { "r": "4.6.2", "os": "mac", "version": "0.1.0", "date": "2026-11-03T18:20:08.000Z", "commit": "7cbb2555d64b81592b23a2eba787702721bc65d0", "fileid": "https://r2.ropensci.org/1334f5ac37f113a7329b68e33bc55c305b424bd62b39a56a2168897c3e6dde3e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41691849296" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.0", "date": "2026-11-03T18:20:25.000Z", "commit": "7cbb2555d64b81592b23a2eba787702721bc65d0", "fileid": "https://r2.ropensci.org/d3e02b7bca83a498dd295eae7a1f738cc36ba6b6f747b5766e88c42d5828d0ab", "status": "success", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41691849296" }, { "r": "4.7.0", "os": "win", "version": "0.1.0", "date": "2026-11-03T18:19:23.000Z", "commit": "7cbb2555d64b81592b23a2eba787702721bc65d0", "fileid": "https://r2.ropensci.org/1e2d0cf756779243ea215aac6e8307e9d6ea4af2760adcafeb9dec025ad7fa95", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41691849296" }, { "r": "4.5.3", "os": "win", "version": "0.1.0", "date": "2026-11-03T18:19:37.000Z", "commit": "7cbb2555d64b81592b23a2eba787702721bc65d0", "fileid": "https://r2.ropensci.org/37fcb6042b05f81e5c403a3da1a134b5161c4ea88909b5a5e1f2c292cde09fed", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41691849296" }, { "r": "4.6.2", "os": "win", "version": "0.1.0", "date": "2026-11-03T18:19:30.000Z", "commit": "7cbb2555d64b81592b23a2eba787702721bc65d0", "fileid": "https://r2.ropensci.org/4aaed0b282a6c8805b2b80bf2ce98d9b7a4858a38677b12fb516feda009429ff", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41691849296" } ] }