From 39da2080690dd059faca3d8a08eb0a71ec59364e Mon Sep 17 00:00:00 2001
From: Jan Valosek <39456460+valosekj@users.noreply.github.com>
Date: Tue, 17 Oct 2023 08:19:12 -0400
Subject: [PATCH] Update README.md

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 README.md | 30 ++++++++++++++++++++++++++++--
 1 file changed, 28 insertions(+), 2 deletions(-)

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 # PAM50 normalized metrics
 
-This repository contains CSV files of spinal cord morphometrics from healthy participants in the PAM50 anatomical space.
+This repository contains CSV files of spinal cord morphometric measures in the PAM50 anatomical space computed from 203 healthy adult volunteers.
 
-The CSV files were generated using [process_data_spine-generic.sh, r20230222](https://github.com/sct-pipeline/dcm-metric-normalization/blob/r20230222/scripts/process_data_spine-generic.sh) script from the [spine-generic/data-multi-subject, r20230223](https://github.com/spine-generic/data-multi-subject/tree/r20230223) dataset.
+👉 Please cite this work if you use it or if you are inspired by it:
+
+```
+Valošek 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
+```
+
+[![DOI](https://neurolibre.org/papers/10.55458/neurolibre.00017/status.svg)](https://doi.org/10.55458/neurolibre.00017)
+
+### Usage
+
+The repository is part of [SCT](https://github.com/spinalcordtoolbox/spinalcordtoolbox/) and is downloaded automatically during SCT installation.
+
+CSV files from this repository are utilized within the following SCT functions:
+
+- `sct_process_segmentation -normalize-PAM50 1`, example:
+
+```console
+sct_process_segmentation -i sub-001_T2w_label-SC_mask.nii.gz -vertfile sub-001_T2w_label-SC_mask_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -o sub-001_T2w_metrics_PAM50.csv
+```
+
+- `sct_compute_compression  -normalize-hc 1`, example: 
+
+```console
+sct_compute_compression -i sub-001_T2w_label-SC_mask.nii.gz -vertfile sub-001_T2w_label-SC_mask_labeled.nii.gz -l sub-001_T2w_label-compression.nii.gz -normalize-hc 1 -o sub-001_T2w_compression_metrics.csv
+```
 
 ### Dependencies
 
 - [SCT v6.0](https://github.com/spinalcordtoolbox/spinalcordtoolbox/tree/6.0)
+
+The CSV files were generated using [process_data_spine-generic.sh, r20230222](https://github.com/sct-pipeline/dcm-metric-normalization/blob/r20230222/scripts/process_data_spine-generic.sh) script from the [spine-generic/data-multi-subject, r20230223](https://github.com/spine-generic/data-multi-subject/tree/r20230223) dataset.