PAM50 normalized metrics

This repository contains morphometric measures in the PAM50 anatomical dimensions computed from 203 healthy adult volunteers.

• spinal_cord directory - CSV files of spinal cord morphometric measures

👉 Please cite this work if you use it or if you are inspired by it:

Valošek, Bédard et al., (2024). A database of the healthy human spinal cord morphometry in the PAM50 template space. Imaging Neuroscience, 2 1–15, https://doi.org/10.1162/imag_a_00075

👉 For interactive figures, please visit the NeuroLibre preprint:

Valošek, Bédard et al., (2023). A database of the healthy human spinal cord morphometry in the PAM50 template space. NeuroLibre Reproducible Preprints, 17, https://doi.org/10.55458/neurolibre.00017

Usage

As part of SCT

The repository is downloaded automatically during the SCT installation.

CSV files from this repository are used by the following SCT functions:

• sct_process_segmentation -normalize-PAM50 1, example:

sct_process_segmentation -i sub-001_T2w_label-SC_seg.nii.gz -vertfile sub-001_T2w_label-SC_seg_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -o sub-001_T2w_metrics_PAM50.csv

• sct_compute_compression -normalize-hc 1, example:

sct_compute_compression -i sub-001_T2w_label-SC_seg.nii.gz -vertfile sub-001_T2w_label-SC_seg_labeled.nii.gz -l sub-001_T2w_label-compression.nii.gz -normalize-hc 1 -o sub-001_T2w_compression_metrics.csv

Standalone usage

If you want to use the morphometric measures outside of SCT in your own research, you can simply download this repository and use the CSV files directly:

git clone https://github.com/spinalcordtoolbox/PAM50-normalized-metrics.git

Details

spinal_cord directory

The CSV files were generated using process_data_spine-generic.sh, r20250320 script from the spine-generic/data-multi-subject, r20250314 dataset. Spinal cord segmentation masks from derivatives/labels were used (files with the label-SC_seg.nii.gz suffix). These masks were produced by sct_deepseg -task seg_sc_contrast_agnostic version 3.1 and visually qc-ed. SCT v7.0 was used to compute the morphometric measures.