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Move spinal cord CSV files to spinal_cord folder (#16)
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* Move CSV files to the `spinal_cord` folder

* README.md: Add details about the `spinal_cord` folder

* README.md: Add a new section with details on "Standalone usage"
valosekj authored Jan 17, 2025
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# PAM50 normalized metrics

This repository contains CSV files of spinal cord morphometric measures in the PAM50 anatomical dimensions computed from 203 healthy adult volunteers.
This repository contains morphometric measures in the [PAM50](https://pubmed.ncbi.nlm.nih.gov/29061527/) 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:

@@ -20,7 +22,9 @@ Valošek, Bédard et al., (2023). A database of the healthy human spinal cord mo

## Usage

The repository is part of [SCT](https://github.com/spinalcordtoolbox/spinalcordtoolbox/) and is downloaded automatically during SCT installation.
### As part of SCT

The repository is downloaded automatically during the [SCT](https://github.com/spinalcordtoolbox/spinalcordtoolbox/) installation.

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

@@ -36,8 +40,19 @@ sct_process_segmentation -i sub-001_T2w_label-SC_mask.nii.gz -vertfile sub-001_T
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
### 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:

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

## Details

- [SCT v6.0](https://github.com/spinalcordtoolbox/spinalcordtoolbox/tree/6.0)
### `spinal_cord` directory

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.
Spinal cord segmentation masks from [derivatives/labels](https://github.com/spine-generic/data-multi-subject/tree/r20230223/derivatives/labels) were used (files with the `seg-manual.nii.gz` suffix). These masks were produced by `sct_deepseg_sc` and manually corrected.
[SCT v6.0](https://github.com/spinalcordtoolbox/spinalcordtoolbox/tree/6.0) was used to compute the morphometric measures.

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1,770 changes: 885 additions & 885 deletions sub-oxfordOhba03_T2w_PAM50.csv → spinal_cord/sub-oxfordOhba03_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-oxfordOhba04_T2w_PAM50.csv → spinal_cord/sub-oxfordOhba04_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-oxfordOhba05_T2w_PAM50.csv → spinal_cord/sub-oxfordOhba05_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-pavia02_T2w_PAM50.csv → spinal_cord/sub-pavia02_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-pavia03_T2w_PAM50.csv → spinal_cord/sub-pavia03_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-pavia04_T2w_PAM50.csv → spinal_cord/sub-pavia04_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-pavia06_T2w_PAM50.csv → spinal_cord/sub-pavia06_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-perform01_T2w_PAM50.csv → spinal_cord/sub-perform01_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-perform02_T2w_PAM50.csv → spinal_cord/sub-perform02_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-perform04_T2w_PAM50.csv → spinal_cord/sub-perform04_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-perform05_T2w_PAM50.csv → spinal_cord/sub-perform05_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-perform06_T2w_PAM50.csv → spinal_cord/sub-perform06_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-queensland01_T2w_PAM50.csv → spinal_cord/sub-queensland01_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-queensland03_T2w_PAM50.csv → spinal_cord/sub-queensland03_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-queensland04_T2w_PAM50.csv → spinal_cord/sub-queensland04_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-queensland05_T2w_PAM50.csv → spinal_cord/sub-queensland05_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-sherbrooke02_T2w_PAM50.csv → spinal_cord/sub-sherbrooke02_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-sherbrooke04_T2w_PAM50.csv → spinal_cord/sub-sherbrooke04_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-sherbrooke05_T2w_PAM50.csv → spinal_cord/sub-sherbrooke05_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-sherbrooke06_T2w_PAM50.csv → spinal_cord/sub-sherbrooke06_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-sherbrooke07_T2w_PAM50.csv → spinal_cord/sub-sherbrooke07_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-stanford01_T2w_PAM50.csv → spinal_cord/sub-stanford01_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-stanford02_T2w_PAM50.csv → spinal_cord/sub-stanford02_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-stanford03_T2w_PAM50.csv → spinal_cord/sub-stanford03_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-stanford04_T2w_PAM50.csv → spinal_cord/sub-stanford04_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-stanford05_T2w_PAM50.csv → spinal_cord/sub-stanford05_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-stanford06_T2w_PAM50.csv → spinal_cord/sub-stanford06_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-strasbourg01_T2w_PAM50.csv → spinal_cord/sub-strasbourg01_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-strasbourg03_T2w_PAM50.csv → spinal_cord/sub-strasbourg03_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-strasbourg04_T2w_PAM50.csv → spinal_cord/sub-strasbourg04_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-strasbourg05_T2w_PAM50.csv → spinal_cord/sub-strasbourg05_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-strasbourg06_T2w_PAM50.csv → spinal_cord/sub-strasbourg06_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-tehranS01_T2w_PAM50.csv → spinal_cord/sub-tehranS01_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-tehranS02_T2w_PAM50.csv → spinal_cord/sub-tehranS02_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-tehranS03_T2w_PAM50.csv → spinal_cord/sub-tehranS03_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-tehranS05_T2w_PAM50.csv → spinal_cord/sub-tehranS05_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-tehranS06_T2w_PAM50.csv → spinal_cord/sub-tehranS06_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-tokyo750w06_T2w_PAM50.csv → spinal_cord/sub-tokyo750w06_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-tokyo750w07_T2w_PAM50.csv → spinal_cord/sub-tokyo750w07_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-tokyoSkyra06_T2w_PAM50.csv → spinal_cord/sub-tokyoSkyra06_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-tokyoSkyra07_T2w_PAM50.csv → spinal_cord/sub-tokyoSkyra07_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ubc01_T2w_PAM50.csv → spinal_cord/sub-ubc01_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ubc02_T2w_PAM50.csv → spinal_cord/sub-ubc02_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ubc03_T2w_PAM50.csv → spinal_cord/sub-ubc03_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ubc04_T2w_PAM50.csv → spinal_cord/sub-ubc04_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ubc05_T2w_PAM50.csv → spinal_cord/sub-ubc05_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ubc06_T2w_PAM50.csv → spinal_cord/sub-ubc06_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ucdavis01_T2w_PAM50.csv → spinal_cord/sub-ucdavis01_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ucdavis03_T2w_PAM50.csv → spinal_cord/sub-ucdavis03_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ucdavis04_T2w_PAM50.csv → spinal_cord/sub-ucdavis04_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ucdavis06_T2w_PAM50.csv → spinal_cord/sub-ucdavis06_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ucdavis07_T2w_PAM50.csv → spinal_cord/sub-ucdavis07_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ucl01_T2w_PAM50.csv → spinal_cord/sub-ucl01_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ucl02_T2w_PAM50.csv → spinal_cord/sub-ucl02_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ucl03_T2w_PAM50.csv → spinal_cord/sub-ucl03_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-ucl06_T2w_PAM50.csv → spinal_cord/sub-ucl06_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-unf03_T2w_PAM50.csv → spinal_cord/sub-unf03_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-unf04_T2w_PAM50.csv → spinal_cord/sub-unf04_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-unf05_T2w_PAM50.csv → spinal_cord/sub-unf05_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-unf06_T2w_PAM50.csv → spinal_cord/sub-unf06_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-unf07_T2w_PAM50.csv → spinal_cord/sub-unf07_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-vallHebron01_T2w_PAM50.csv → spinal_cord/sub-vallHebron01_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-vallHebron02_T2w_PAM50.csv → spinal_cord/sub-vallHebron02_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-vallHebron03_T2w_PAM50.csv → spinal_cord/sub-vallHebron03_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-vallHebron04_T2w_PAM50.csv → spinal_cord/sub-vallHebron04_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-vallHebron05_T2w_PAM50.csv → spinal_cord/sub-vallHebron05_T2w_PAM50.csv

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1,770 changes: 885 additions & 885 deletions sub-vallHebron06_T2w_PAM50.csv → spinal_cord/sub-vallHebron06_T2w_PAM50.csv

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