An end-to-end R pipeline for longitudinal MRI and CT analysis in spinal cord injury (SCI) research. Provides R wrappers for the Spinal Cord Toolbox (SCT), DICOM tools, SCI-specific clinical metrics, and pipeline orchestration with built-in quality control.
Install from GitHub:
# install.packages("pak")
pak::pak("rabanheller/scimagR")scimagR requires the following external tools:
| Tool | Version | Purpose |
|---|---|---|
| Spinal Cord Toolbox | >= 6.4 | Segmentation, labeling, parameter extraction |
| dcm2niix | any | DICOM to NIfTI conversion |
| Python 3 + pydicom | any | DICOM metadata extraction & anonymization |
Verify installation:
library(scimagR)
check_sct()
check_dcm2niix()
check_pydicom()library(scimagR)
# 1. Create a new project
sci_create_project(
"~/projects/my-sci-study",
title = "Cervical SCI Longitudinal MRI",
author = "Your Name"
)
# 2. Place DICOMs in data/raw/dicom/, fill registry CSVs
# 3. Run the pipeline
sci_run_pipeline("~/projects/my-sci-study")| Module | Key Functions | Description |
|---|---|---|
| SCT Interface | sct_segment_sc(), sct_segment_lesion(), sct_label_vertebrae() |
R wrappers for all SCT CLI commands |
| DICOM Tools | extract_dicom_metadata(), anonymize_dicom(), convert_dcm2niix() |
Metadata extraction, anonymization, conversion |
| SCI Metrics | compute_mscc(), compute_compression_ratio(), classify_phase() |
Domain-specific clinical measures |
| Registry | create_registry(), validate_registry(), coverage_matrix() |
Structured time-point tracking |
| QC System | filter_evaluable(), log_exclusion(), integrity_summary() |
Artifact grading and exclusion tracking |
| Visualization | theme_sci(), scale_colour_phase(), plot_violin_box() |
Publication-ready figures |
| Pipeline | sci_run_pipeline(), sci_pipeline_status() |
Orchestration with resume support |
| Scaffold | sci_create_project() |
Workflowr project setup |
If you use scimagR in your research, please cite:
Heller R (2026). scimagR: Spinal Cord Injury Imaging Pipeline for MRI and
CT Analysis in R. R package version 0.1.0.
https://github.com/rabanheller/scimagR
MIT