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# PAM50 normalized metrics | ||
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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. | ||
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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: | ||
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``` | ||
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 | ||
``` | ||
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[![DOI](https://neurolibre.org/papers/10.55458/neurolibre.00017/status.svg)](https://doi.org/10.55458/neurolibre.00017) | ||
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### Usage | ||
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The repository is part of [SCT](https://github.com/spinalcordtoolbox/spinalcordtoolbox/) and is downloaded automatically during SCT installation. | ||
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CSV files from this repository are utilized within the following SCT functions: | ||
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- `sct_process_segmentation -normalize-PAM50 1`, example: | ||
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```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 | ||
``` | ||
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- `sct_compute_compression -normalize-hc 1`, example: | ||
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```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 | ||
``` | ||
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### Dependencies | ||
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- [SCT v6.0](https://github.com/spinalcordtoolbox/spinalcordtoolbox/tree/6.0) | ||
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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. |