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.
If you have any questions regarding the module content please ask them in the relevant module channel on the school Discord server. If you do not have access to the server and would like to join, please send us an email at school [dot] brainhack [at] gmail [dot] com.
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:
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 your local TA(s) to validate you completed the exercises correctly.
🎉 🎉 🎉 you completed this training module! 🎉 🎉 🎉
If you want to learn more about BIDS and pybids, check: