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bids_tools

code for BIDS data processing

https://github.com/pamcconnell/bids_tools

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (3.4%) to scientific vocabulary
Last synced: 8 months ago · JSON representation ·

Repository

code for BIDS data processing

Basic Info
  • Host: GitHub
  • Owner: PAmcconnell
  • Language: Python
  • Default Branch: main
  • Size: 3.65 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 2
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed about 2 years ago
Metadata Files
Readme Citation

README.md

BIDS_tools

code for BIDS data processing / inputs: dicomrootdir or physiorootdir, bidsrootdir

assumes BIDS compliant directory structure (where 'BIDS' is project/dataset root directory):

/BIDS/code /BIDS/doc /BIDS/doc/logs /BIDS/derivatives /BIDS/sourcedata/ (dicomrootdir - dicom zip archive path)) + /sub-/ses-/dicom -> dicomsorted /BIDS/sourcedata/sub-/ses-/physio (physiorootdir) /BIDS/sourcedata/sub-/ses-/beh (behrootdir) /BIDS/dataset (bidsroot_dir)

usage

Sort Dicoms - ses-1

python ~/Documents/MATLAB/software/iNR/BIDStools/BIDSsortdicomfiles.py ~/Documents/MRI/LEARN/BIDS_test/sourcedata/sub-LRN001/ses-1

Process dicom to nifti BIDs ses-1

python ~/Documents/MATLAB/software/iNR/BIDStools/BIDSprocessses-1.py ~/Documents/MRI/LEARN/BIDStest/sourcedata/ --start-id sub-LRN001 --end-id sub-LRN00x [--pydeface]

Sort Dicoms - ses-2

python ~/Documents/MATLAB/software/iNR/BIDStools/sortdicomfiles.py ~/Documents/MRI/LEARN/BIDStest/sourcedata/sub-LRN001/ses-2

Process dicom to nifti BIDs ses-2

python ~/Documents/MATLAB/software/iNR/BIDStools/BIDSprocessses-2.py ~/Documents/MRI/LEARN/BIDStest/sourcedata/ --start-id sub-LRN001 --end-id sub-LRN00x [--pydeface]

Process physio to BIDS - ses-1

python ~/Documents/MATLAB/software/iNR/BIDStools/BIDSprocessphysioses1.py ~/Documents/MRI/LEARN/BIDStest/sourcedata/sub-LRN001/ses-1/physio/ ~/Documents/MRI/LEARN/BIDS_test/dataset [--force]

Process physio to BIDS - ses-2

python ~/Documents/MATLAB/software/iNR/BIDStools/BIDSprocessphysioses2.py ~/Documents/MRI/LEARN/BIDStest/sourcedata/sub-LRN001/ses-2/physio/ ~/Documents/MRI/LEARN/BIDS_test/dataset [--force]

Owner

  • Name: Patrick A. McConnell
  • Login: PAmcconnell
  • Kind: user
  • Location: San Francisco, CA
  • Company: University of California San Francisco

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
authors:
- family-names: "McConnell"
  given-names: "Patrick A."
  orcid: "https://orcid.org/0000-0002-6367-7065"
title: "BIDS_tools"
version: 1.0.0
doi: 10.5281/zenodo.1234
date-released: 2024-01-02
url: "https://github.com/iNRLab/BIDS_tools"

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