Package index • scimagR

All functions

anonymize_dicom(): Anonymize DICOM Files
check_dcm2niix(): Check dcm2niix Availability
check_pydicom(): Check pydicom Availability
check_sct(): Check Spinal Cord Toolbox Availability
classify_artifact(): Classify MRI Artifact Grade
classify_phase(): Classify SCI Phase Based on Days Post Trauma
compute_compression_ratio(): Compute Spinal Cord Compression Ratio
compute_csa_ratio(): Compute Cross-Sectional Area Ratio
compute_mscc(): Compute Maximum Spinal Cord Compression (MSCC)
convert_batch(): Batch Convert DICOM to NIfTI
convert_dcm2niix(): Convert DICOM to NIfTI
coverage_matrix(): Create a Modality Coverage Matrix
create_qc_log(): Create a QC Segmentation Log
create_registry(): Create an Imaging Registry from DICOM Metadata
extract_dicom_metadata(): Extract DICOM Header Metadata
filter_evaluable(): Filter to Evaluable Imaging Sessions
integrity_summary(): Print Data Integrity Summary
log_exclusion(): Log an Exclusion Step
pal_artifact: Artifact Grade Colour Palette
pal_modality: Modality Colour Palette
pal_phase: SCI Phase Colour Palette
plot_coverage(): Plot Modality Coverage Matrix
plot_forest(): Forest Plot
plot_spaghetti(): Spaghetti Plot
plot_violin_box(): Violin + Box Plot
save_fig(): Save Figure with Standard Conventions
save_rds(): Save R Object as RDS
save_table(): Save Table as Excel
scale_colour_artifact() scale_fill_artifact(): Colour and Fill Scales for Artifact Grades
scale_colour_modality() scale_fill_modality(): Colour and Fill Scales for Imaging Modalities
scale_colour_phase() scale_fill_phase(): Colour and Fill Scales for SCI Phases
sci_create_project(): Create a New SCI MRI/CT Analysis Project
sci_pipeline_status(): Get Pipeline Status
sci_run_pipeline(): Run the SCI Analysis Pipeline
sct_analyze_lesion(): Extract Lesion Parameters
sct_generate_qc(): Generate SCT Quality Control Report
sct_label_vertebrae(): Label Vertebral Levels
sct_process_segmentation(): Extract Morphometric Parameters
sct_segment_lesion(): Segment SCI Lesion
sct_segment_sc(): Segment Spinal Cord
theme_sci(): SCI Publication Theme
update_qc_log(): Update a QC Log
validate_qc_log(): Validate a QC Log
validate_registry(): Validate an Imaging Registry