The brain imaging data standards and applications
The estimated time to complete this training module is 2h.
The prerequisites to take this module are:
- the installation module.
- the introduction to the terminal module.
- the python for data analysis module. Contact Natasha Clarke if you have questions on this module, or if you want to check that you completed successfully all the exercises.
This module was presented by Christopher J. Markiewicz during the QLSC 612 course in 2020.
The slides are available here.
The video of his presentation is available below:
- Download a few subjects (n=3) from the dataset DS000228 on openneuro. Hint: the dataset is available with datalad from this git repository.
- Check that the resulting folder is a bids-compliant dataset using the bids validator (using a web browser or a local
npminstall). Did you get any warnings? Explain what they are and whether they are a concern.
- Install pybids. Use pybids to get a list of all BOLD
nii.gzfiles for subject
pixar003. In which folder did you find them? is it logical? You may want to have a look at the BIDS documentation to familiarize yourself with the BIDS standard.
- Using pybids, get a list of the flip angles in
- Clone a Midnight Brain Scan dataset from this git repository. Use
pybidsto load the
participant.tsvfile as a pandas dataframe in python.
- Follow up with Natasha Clarke to validate you completed the exercise correctly.
- 🎉 🎉 🎉 you completed this training module! 🎉 🎉 🎉
If you want to learn more about BIDS and pybids, check:
- the BIDS Starter Kit,
- the BIDS documentation,
- the dicom2bids converter - we have local support for this one.
- the pybids documentation