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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.

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