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BIDS validator and linter

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CPP_BIDS

• CPP_BIDS
• Output format
  • Modality agnostic aspect
• Documentation
• Contributing
  • Guidestyle
  • BIDS naming convention
  • Change log
  • Contributors ✨

A set of function for matlab and octave to create BIDS-compatible folder structure and filenames for the output of behavioral, EEG, fMRI, eyetracking studies.

Output format

Modality agnostic aspect

Subjects, session and run number labels will be numbers with zero padding up to 3 values (e.g subject 1 will become sub-001).

A session folder will ALWAYS be created even if not requested (default will be ses-001).

Task labels will be printed in camelCase in the filenames.

Time stamps are added directly in the filename by adding a suffix _date-YYYYMMDDHHMM which makes the file name non-BIDS compliant. This was added to prevent overwriting files in case a certain run needs to be done a second time because of a crash (Some of us are paranoid about keeping even cancelled runs during my experiments). This suffix should be removed to make the data set BIDS compliant. See convertSourceToRaw.m for more details.

For example:

sub-090/ses-003/sub-090_ses-003_task-auditoryTask_run-023_events_date-202007291536.tsv

Documentation

• Installation
• How to use it: jupyter notebooks
• Functions description

Contributing

Feel free to open issues to report a bug and ask for improvements.

If you want to contribute, have a look at our contributing guidelines that are meant to guide you and help you get started. If something is not clear or you get stuck: it is more likely we did not do good enough a job at explaining things. So do not hesitate to open an issue, just to ask for clarification.

Guidestyle

• We use camelCase.

• We keep the McCabe complexity as reported by the check_my_code function below 15.

• We use the MISS_HIT linter to automatically fix some linting issues.

BIDS naming convention

Here are the naming templates used.

• Behavior

sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.tsv
sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.json
sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_beh.tsv
sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_beh.json

• BOLD

sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]

• iEEG

sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json

• EEG

sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>
sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.json

• MEG

???

• Eyetracker

current format <matches>_recording-eyetracking_physio.tsv.gz

future BEP format in a dedicated eyetracker folder

sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>

• Stim and physio

<matches>[_recording-<label>]_physio.tsv.gz
<matches>[_recording-<label>]_physio.json
<matches>[_recording-<label>]_stim.tsv.gz
<matches>[_recording-<label>]_stim.json

Change log

Contributors ✨

Thanks goes to these wonderful people (emoji key):

CerenB 💻 🎨 📖 📓 🤔 🐛

marcobarilari 💻 🎨 📖 📓 🤔 🐛

Remi Gau 💻 🎨 📖 🐛 📓 🤔 🚇 🚧 ⚠️ 💬

This project follows the all-contributors specification. Contributions of any kind welcome!