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notebooks
notebooks
 
 
statistics
statistics
 
 
.gitignore
.gitignore
 
 
README.md
README.md
 
 
participants.tsv
participants.tsv
 
 
requirements.txt
requirements.txt
 
 
sub-amu01_T2w_PAM50.csv
sub-amu01_T2w_PAM50.csv
 
 
sub-amu02_T2w_PAM50.csv
sub-amu02_T2w_PAM50.csv
 
 
sub-amu03_T2w_PAM50.csv
sub-amu03_T2w_PAM50.csv
 
 
sub-amu04_T2w_PAM50.csv
sub-amu04_T2w_PAM50.csv
 
 
sub-amu05_T2w_PAM50.csv
sub-amu05_T2w_PAM50.csv
 
 
sub-balgrist01_T2w_PAM50.csv
sub-balgrist01_T2w_PAM50.csv
 
 
sub-balgrist02_T2w_PAM50.csv
sub-balgrist02_T2w_PAM50.csv
 
 
sub-balgrist03_T2w_PAM50.csv
sub-balgrist03_T2w_PAM50.csv
 
 
sub-balgrist04_T2w_PAM50.csv
sub-balgrist04_T2w_PAM50.csv
 
 
sub-balgrist05_T2w_PAM50.csv
sub-balgrist05_T2w_PAM50.csv
 
 
sub-balgrist06_T2w_PAM50.csv
sub-balgrist06_T2w_PAM50.csv
 
 
sub-barcelona05_T2w_PAM50.csv
sub-barcelona05_T2w_PAM50.csv
 
 
sub-barcelona06_T2w_PAM50.csv
sub-barcelona06_T2w_PAM50.csv
 
 
sub-beijingGE01_T2w_PAM50.csv
sub-beijingGE01_T2w_PAM50.csv
 
 
sub-beijingGE02_T2w_PAM50.csv
sub-beijingGE02_T2w_PAM50.csv
 
 
sub-beijingGE03_T2w_PAM50.csv
sub-beijingGE03_T2w_PAM50.csv
 
 
sub-beijingPrisma01_T2w_PAM50.csv
sub-beijingPrisma01_T2w_PAM50.csv
 
 
sub-beijingPrisma04_T2w_PAM50.csv
sub-beijingPrisma04_T2w_PAM50.csv
 
 
sub-beijingPrisma05_T2w_PAM50.csv
sub-beijingPrisma05_T2w_PAM50.csv
 
 
sub-beijingVerio01_T2w_PAM50.csv
sub-beijingVerio01_T2w_PAM50.csv
 
 
sub-beijingVerio02_T2w_PAM50.csv
sub-beijingVerio02_T2w_PAM50.csv
 
 
sub-beijingVerio03_T2w_PAM50.csv
sub-beijingVerio03_T2w_PAM50.csv
 
 
sub-brnoCeitec01_T2w_PAM50.csv
sub-brnoCeitec01_T2w_PAM50.csv
 
 
sub-brnoCeitec02_T2w_PAM50.csv
sub-brnoCeitec02_T2w_PAM50.csv
 
 
sub-brnoCeitec03_T2w_PAM50.csv
sub-brnoCeitec03_T2w_PAM50.csv
 
 
sub-brnoCeitec05_T2w_PAM50.csv
sub-brnoCeitec05_T2w_PAM50.csv
 
 
sub-brnoCeitec06_T2w_PAM50.csv
sub-brnoCeitec06_T2w_PAM50.csv
 
 
sub-brnoUhb01_T2w_PAM50.csv
sub-brnoUhb01_T2w_PAM50.csv
 
 
sub-brnoUhb02_T2w_PAM50.csv
sub-brnoUhb02_T2w_PAM50.csv
 
 
sub-brnoUhb03_T2w_PAM50.csv
sub-brnoUhb03_T2w_PAM50.csv
 
 
sub-brnoUhb04_T2w_PAM50.csv
sub-brnoUhb04_T2w_PAM50.csv
 
 
sub-brnoUhb05_T2w_PAM50.csv
sub-brnoUhb05_T2w_PAM50.csv
 
 
sub-brnoUhb06_T2w_PAM50.csv
sub-brnoUhb06_T2w_PAM50.csv
 
 
sub-brnoUhb07_T2w_PAM50.csv
sub-brnoUhb07_T2w_PAM50.csv
 
 
sub-brnoUhb08_T2w_PAM50.csv
sub-brnoUhb08_T2w_PAM50.csv
 
 
sub-cardiff01_T2w_PAM50.csv
sub-cardiff01_T2w_PAM50.csv
 
 
sub-cardiff02_T2w_PAM50.csv
sub-cardiff02_T2w_PAM50.csv
 
 
sub-cardiff03_T2w_PAM50.csv
sub-cardiff03_T2w_PAM50.csv
 
 
sub-cardiff04_T2w_PAM50.csv
sub-cardiff04_T2w_PAM50.csv
 
 
sub-cmrra01_T2w_PAM50.csv
sub-cmrra01_T2w_PAM50.csv
 
 
sub-cmrra02_T2w_PAM50.csv
sub-cmrra02_T2w_PAM50.csv
 
 
sub-cmrra03_T2w_PAM50.csv
sub-cmrra03_T2w_PAM50.csv
 
 
sub-cmrra04_T2w_PAM50.csv
sub-cmrra04_T2w_PAM50.csv
 
 
sub-cmrra05_T2w_PAM50.csv
sub-cmrra05_T2w_PAM50.csv
 
 
sub-cmrra06_T2w_PAM50.csv
sub-cmrra06_T2w_PAM50.csv
 
 
sub-cmrrb01_T2w_PAM50.csv
sub-cmrrb01_T2w_PAM50.csv
 
 
sub-cmrrb02_T2w_PAM50.csv
sub-cmrrb02_T2w_PAM50.csv
 
 
sub-cmrrb03_T2w_PAM50.csv
sub-cmrrb03_T2w_PAM50.csv
 
 
sub-cmrrb04_T2w_PAM50.csv
sub-cmrrb04_T2w_PAM50.csv
 
 
sub-cmrrb07_T2w_PAM50.csv
sub-cmrrb07_T2w_PAM50.csv
 
 
sub-dresden01_T2w_PAM50.csv
sub-dresden01_T2w_PAM50.csv
 
 
sub-dresden02_T2w_PAM50.csv
sub-dresden02_T2w_PAM50.csv
 
 
sub-fslAchieva01_T2w_PAM50.csv
sub-fslAchieva01_T2w_PAM50.csv
 
 
sub-fslAchieva02_T2w_PAM50.csv
sub-fslAchieva02_T2w_PAM50.csv
 
 
sub-fslAchieva03_T2w_PAM50.csv
sub-fslAchieva03_T2w_PAM50.csv
 
 
sub-fslAchieva04_T2w_PAM50.csv
sub-fslAchieva04_T2w_PAM50.csv
 
 
sub-fslAchieva05_T2w_PAM50.csv
sub-fslAchieva05_T2w_PAM50.csv
 
 
sub-fslPrisma01_T2w_PAM50.csv
sub-fslPrisma01_T2w_PAM50.csv
 
 
sub-fslPrisma03_T2w_PAM50.csv
sub-fslPrisma03_T2w_PAM50.csv
 
 
sub-fslPrisma04_T2w_PAM50.csv
sub-fslPrisma04_T2w_PAM50.csv
 
 
sub-fslPrisma05_T2w_PAM50.csv
sub-fslPrisma05_T2w_PAM50.csv
 
 
sub-fslPrisma06_T2w_PAM50.csv
sub-fslPrisma06_T2w_PAM50.csv
 
 
sub-geneva01_T2w_PAM50.csv
sub-geneva01_T2w_PAM50.csv
 
 
sub-geneva02_T2w_PAM50.csv
sub-geneva02_T2w_PAM50.csv
 
 
sub-geneva03_T2w_PAM50.csv
sub-geneva03_T2w_PAM50.csv
 
 
sub-geneva04_T2w_PAM50.csv
sub-geneva04_T2w_PAM50.csv
 
 
sub-geneva05_T2w_PAM50.csv
sub-geneva05_T2w_PAM50.csv
 
 
sub-hamburg01_T2w_PAM50.csv
sub-hamburg01_T2w_PAM50.csv
 
 
sub-hamburg03_T2w_PAM50.csv
sub-hamburg03_T2w_PAM50.csv
 
 
sub-hamburg04_T2w_PAM50.csv
sub-hamburg04_T2w_PAM50.csv
 
 
sub-hamburg06_T2w_PAM50.csv
sub-hamburg06_T2w_PAM50.csv
 
 
sub-juntendo750w01_T2w_PAM50.csv
sub-juntendo750w01_T2w_PAM50.csv
 
 
sub-juntendo750w02_T2w_PAM50.csv
sub-juntendo750w02_T2w_PAM50.csv
 
 
sub-juntendo750w05_T2w_PAM50.csv
sub-juntendo750w05_T2w_PAM50.csv
 
 
sub-juntendo750w06_T2w_PAM50.csv
sub-juntendo750w06_T2w_PAM50.csv
 
 
sub-mgh01_T2w_PAM50.csv
sub-mgh01_T2w_PAM50.csv
 
 
sub-mgh02_T2w_PAM50.csv
sub-mgh02_T2w_PAM50.csv
 
 
sub-mgh04_T2w_PAM50.csv
sub-mgh04_T2w_PAM50.csv
 
 
sub-mgh05_T2w_PAM50.csv
sub-mgh05_T2w_PAM50.csv
 
 
sub-mgh06_T2w_PAM50.csv
sub-mgh06_T2w_PAM50.csv
 
 
sub-milan01_T2w_PAM50.csv
sub-milan01_T2w_PAM50.csv
 
 
sub-milan02_T2w_PAM50.csv
sub-milan02_T2w_PAM50.csv
 
 
sub-milan03_T2w_PAM50.csv
sub-milan03_T2w_PAM50.csv
 
 
sub-milan04_T2w_PAM50.csv
sub-milan04_T2w_PAM50.csv
 
 
sub-milan05_T2w_PAM50.csv
sub-milan05_T2w_PAM50.csv
 
 
sub-milan06_T2w_PAM50.csv
sub-milan06_T2w_PAM50.csv
 
 
sub-milan07_T2w_PAM50.csv
sub-milan07_T2w_PAM50.csv
 
 
sub-mniPilot1_T2w_PAM50.csv
sub-mniPilot1_T2w_PAM50.csv
 
 
sub-mniS01_T2w_PAM50.csv
sub-mniS01_T2w_PAM50.csv
 
 
sub-mniS02_T2w_PAM50.csv
sub-mniS02_T2w_PAM50.csv
 
 
sub-mniS03_T2w_PAM50.csv
sub-mniS03_T2w_PAM50.csv
 
 
sub-mniS04_T2w_PAM50.csv
sub-mniS04_T2w_PAM50.csv
 
 
sub-mniS07_T2w_PAM50.csv
sub-mniS07_T2w_PAM50.csv
 
 
sub-mniS08_T2w_PAM50.csv
sub-mniS08_T2w_PAM50.csv
 
 

Repository files navigation

PAM50 normalized metrics

This repository contains CSV files of spinal cord morphometric measures in the PAM50 anatomical dimensions computed from 203 healthy adult volunteers.

👉 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

DOI

👉 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

DOI

Usage

The repository is part of SCT and is downloaded automatically during 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_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:
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

The CSV files were generated using process_data_spine-generic.sh, r20230222 script from the spine-generic/data-multi-subject, r20230223 dataset.

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Spinal cord morphometry in the PAM50 template space

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