Package: scimagR 0.1.0

R. Heller

scimagR: Spinal Cord Injury Imaging Pipeline for MRI and CT Analysis in R

An end-to-end pipeline for longitudinal MRI and CT analysis in spinal cord injury (SCI) research. Provides R wrappers for the Spinal Cord Toolbox (SCT) including SCIsegV2 lesion segmentation, DICOM anonymization and NIfTI conversion tools, SCI-specific clinical metrics (MSCC, compression ratio, tissue bridge quantification), implant artifact grading, and pipeline orchestration with built-in quality control. Integrates with workflowr for reproducible, publication-ready neuroimaging analyses.

Authors:R. Heller [aut, cre]

scimagR_0.1.0.tar.gz
scimagR_0.1.0.zip(r-4.7-any)scimagR_0.1.0.zip(r-4.6-any)scimagR_0.1.0.zip(r-4.5-any)
scimagR_0.1.0.tgz(r-4.6-any)scimagR_0.1.0.tgz(r-4.5-any)
scimagR_0.1.0.tar.gz(r-4.7-any)scimagR_0.1.0.tar.gz(r-4.6-any)
scimagR_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scimagR/json (API)

# Install 'scimagR' in R:
install.packages('scimagR', repos = c('https://cttir.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cttir/scimagr/issues

On CRAN:

Conda:

4.18 score 6 scripts 47 exports 40 dependencies

Last updated from:4c440bf691. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK141
source / vignettesOK223
linux-releaseOK144
macos-releaseOK110
macos-oldrelOK96
windows-develOK89
windows-releaseOK115
windows-oldrelOK69
wasm-releaseOK102

Exports:anonymize_dicomcheck_dcm2niixcheck_pydicomcheck_sctclassify_artifactclassify_phasecompute_compression_ratiocompute_csa_ratiocompute_msccconvert_batchconvert_dcm2niixcoverage_matrixcreate_qc_logcreate_registryextract_dicom_metadatafilter_evaluableintegrity_summarylog_exclusionpal_artifactpal_modalitypal_phaseplot_coverageplot_forestplot_spaghettiplot_violin_boxsave_figsave_rdssave_tablescale_colour_artifactscale_colour_modalityscale_colour_phasescale_fill_artifactscale_fill_modalityscale_fill_phasesci_create_projectsci_pipeline_statussci_run_pipelinesct_analyze_lesionsct_generate_qcsct_label_vertebraesct_process_segmentationsct_segment_lesionsct_segment_sctheme_sciupdate_qc_logvalidate_qc_logvalidate_registry

Dependencies:bitbit64clicliprcpp11crayondplyrfarvergenericsggplot2gluegtablehmsisobandlabelinglifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerreadrrlangS7scalesstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrwritexl

Getting Started with scimagR
Overview | Prerequisites | Creating a Project | Data Organization | Running the Pipeline | Computing SCI Metrics | Visualization
Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-05-04

Pipeline Walkthrough
Overview | Pipeline Steps | Running the Full Pipeline | Running Individual Steps | The QC Pause | Checking Pipeline Status | Artifact Grading Strategy | Coverage Matrix | Resuming After Interruption
Rendered frompipeline-walkthrough.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-05-04

SCT Interface
Overview | Configuration | Spinal Cord Segmentation | Lesion Segmentation (SCIsegV2) | Vertebral Labeling | Parameter Extraction | QC Reports | Idempotent Execution | Troubleshooting
Rendered fromsct-interface.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-05-04

Readme and manuals

Help Manual

Help pageTopics
Anonymize DICOM Filesanonymize_dicom
Check dcm2niix Availabilitycheck_dcm2niix
Check pydicom Availabilitycheck_pydicom
Check Spinal Cord Toolbox Availabilitycheck_sct
Classify MRI Artifact Gradeclassify_artifact
Classify SCI Phase Based on Days Post Traumaclassify_phase
Compute Spinal Cord Compression Ratiocompute_compression_ratio
Compute Cross-Sectional Area Ratiocompute_csa_ratio
Compute Maximum Spinal Cord Compression (MSCC)compute_mscc
Batch Convert DICOM to NIfTIconvert_batch
Convert DICOM to NIfTIconvert_dcm2niix
Create a Modality Coverage Matrixcoverage_matrix
Create a QC Segmentation Logcreate_qc_log
Create an Imaging Registry from DICOM Metadatacreate_registry
Extract DICOM Header Metadataextract_dicom_metadata
Filter to Evaluable Imaging Sessionsfilter_evaluable
Print Data Integrity Summaryintegrity_summary
Log an Exclusion Steplog_exclusion
Artifact Grade Colour Palettepal_artifact
Modality Colour Palettepal_modality
SCI Phase Colour Palettepal_phase
Plot Modality Coverage Matrixplot_coverage
Forest Plotplot_forest
Spaghetti Plotplot_spaghetti
Violin + Box Plotplot_violin_box
Save Figure with Standard Conventionssave_fig
Save R Object as RDSsave_rds
Save Table as Excelsave_table
Colour and Fill Scales for Artifact Gradesscale_artifact scale_colour_artifact scale_fill_artifact
Colour and Fill Scales for Imaging Modalitiesscale_colour_modality scale_fill_modality scale_modality
Colour and Fill Scales for SCI Phasesscale_colour_phase scale_fill_phase scale_phase
Create a New SCI MRI/CT Analysis Projectsci_create_project
Get Pipeline Statussci_pipeline_status
Run the SCI Analysis Pipelinesci_run_pipeline
Extract Lesion Parameterssct_analyze_lesion
Generate SCT Quality Control Reportsct_generate_qc
Label Vertebral Levelssct_label_vertebrae
Extract Morphometric Parameterssct_process_segmentation
Segment SCI Lesionsct_segment_lesion
Segment Spinal Cordsct_segment_sc
SCI Publication Themetheme_sci
Update a QC Logupdate_qc_log
Validate a QC Logvalidate_qc_log
Validate an Imaging Registryvalidate_registry