[WIP][ENH] BIDSify filenames and tables #43
Draft
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
=== Do not change lines below ===
{
"chain": [],
"cmd": "find atlases/mask -type f | rename 's/.nii.gz/_mask.nii.gz/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
=== Do not change lines below ===
{
"chain": [],
"cmd": "find atlases/mask -type f | rename 's/_res_/_res-/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
=== Do not change lines below ===
{
"chain": [],
"cmd": "find atlases/mask -type f | rename 's/_descr-/_desc-/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
=== Do not change lines below ===
{
"chain": [],
"cmd": "find atlases/mask -type f | rename 's/_desc-brainmask/_desc-brain/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
=== Do not change lines below ===
{
"chain": [],
"cmd": "find atlases/mask -type f -name 'MNI*' | rename 's/MNI152NLin6/space-MNI152NLin6/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
=== Do not change lines below ===
{
"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": "."
}
^^^ Do not change lines above ^^^
=== 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": "."
}
^^^ Do not change lines above ^^^
=== Do not change lines below ===
{
"chain": [],
"cmd": "find atlases/mask -type f | rename 's/_T1w_/T1w/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
=== Do not change lines below ===
{
"chain": [],
"cmd": "find atlases/reference_brains -type f | rename 's/_T1w_descr-brain/_desc-brain_T1w/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
=== 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": "."
}
^^^ Do not change lines above ^^^
=== Do not change lines below ===
{
"chain": [],
"cmd": "find atlases/reference_brains -type f | rename 's/FSL/atlas-FSL/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
=== 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": "."
}
^^^ Do not change lines above ^^^
=== Do not change lines below ===
{
"chain": [],
"cmd": "find atlases/label/Human -type f | rename 's/.nii.gz/_dseg.nii.gz/g'",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
=== Do not change lines below ===
{
"chain": [],
"cmd": "cd atlases/label/Human/ && bash add_label_entity.sh",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
=== Do not change lines below ===
{
"chain": [],
"cmd": "python3 rename.py",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
=== Do not change lines below ===
{
"chain": [],
"cmd": "python3 clean_up_json.py",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
=== Do not change lines below ===
{
"chain": [],
"cmd": "python3 add_hemisphere_to_tsv.py",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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