[WIP][ENH] BIDSify filenames and tables #43
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{
"chain": [],
"cmd": "find atlases/mask -type f | rename 's/.nii.gz/_mask.nii.gz/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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{
"chain": [],
"cmd": "find atlases/mask -type f | rename 's/_res_/_res-/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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{
"chain": [],
"cmd": "find atlases/mask -type f | rename 's/_descr-/_desc-/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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{
"chain": [],
"cmd": "find atlases/mask -type f | rename 's/_desc-brainmask/_desc-brain/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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{
"chain": [],
"cmd": "find atlases/mask -type f -name 'MNI*' | rename 's/MNI152NLin6/space-MNI152NLin6/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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{
"chain": [],
"cmd": "find atlases/mask -type f -name 'Corpus*' | rename 's/_mask.nii.gz/_desc-CorpusCallosum_mask.nii.gz/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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=== Do not change lines below ===
{
"chain": [],
"cmd": "find atlases/mask -type f -name 'Corpus*' | rename 's/CorpusCallosum_res/res/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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{
"chain": [],
"cmd": "find atlases/mask -type f | rename 's/_T1w_/T1w/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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{
"chain": [],
"cmd": "find atlases/reference_brains -type f | rename 's/_T1w_descr-brain/_desc-brain_T1w/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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=== Do not change lines below ===
{
"chain": [],
"cmd": "find atlases/reference_brains -type f | rename 's/MNI/atlas-MNI/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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{
"chain": [],
"cmd": "find atlases/reference_brains -type f | rename 's/FSL/atlas-FSL/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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=== Do not change lines below ===
{
"chain": [],
"cmd": "find atlases/reference_brains -type f | rename 's/atlas-MNI152_T1_4mm_symmetric.nii/atlas-MNI152_res-4mm_desc-symmetric_T1w.nii/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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{
"chain": [],
"cmd": "find atlases/label/Human -type f | rename 's/.nii.gz/_dseg.nii.gz/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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{
"chain": [],
"cmd": "cd atlases/label/Human/ && bash add_label_entity.sh",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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{
"chain": [],
"cmd": "python3 rename.py",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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{
"chain": [],
"cmd": "python3 clean_up_json.py",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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{
"chain": [],
"cmd": "python3 add_hemisphere_to_tsv.py",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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closes #37
Aim
Make the filenames BIDS friendly and make sure the tables and metadata are more BIDS compliant.
TODO
HarvardOxford-thr25_*_variant-lateral-ventricles_*iSUMMARY
Executed through the following command