Material for the OHBM 2023 Educational Course Tutorial "Hands (and sensors!) on: a practical guide to acquiring your own physiological data"

This repository contains installation materials, data, and code for the tutorial "Hands (and sensors!) on: a practical guide to acquiring your own physiological data" at the OHBM 2023 Educational Course "Physiologic fMRI signals: friend or foe? How and why to measure, model, and account for physiology". You can find links to other tutorials in this course here.

Thank you to Stefano Moia for help in preparing the installation instructions for this tutorial! You can also find more comprehensive documentation for installing and using phys2bids here.

Laptop set-up

To follow this tutorial, you will need a laptop, requiring a little bit of setup beforehand.

To start: set up your own installation!

0. Prerequisites

You will need a laptop with python installed, as well as pip. Python version should be 3.7 or above. You also need to download the files in this repository, either zipped in a package or by locally cloning the repository.

1. Virtual environment

The best way to ensure the software will function without changing anything in your system is using a virtual environment. For that, first install virtualenv::

pip install -U virtualenv

(Note you might need to use pip3 instead of pip, depending on your OS and setup, to work with python 3)

Then, create and activate the virtual environment - in this case I called it OHBM2023phys2bids, but you can use a different name:

virtualenv OHBM2023phys2bids
source OHBM2023phys2bids/bin/activate

Note that the first command above will create a folder where you called it from, and the second command assumes this is the case - if you want you can specify a different path though.

Once you activated the virtual environment, you can proceed with package installation.

2. Package installation

To install the phys2bids software for this tutorial, you should run the following command:

pip install phys2bids[acq]

Here, [acq] specifies that we are also installing the bioread module, which adds support for loading .acq files.

3. Check your installation

Run:

phys2bids -v

I am running 'phys2bids 2.10.0' for this tutorial!

4. Get to know phys2bids

You can find all the information you need to interact with phys2bids from the commandline by running:

phys2bids -h

or

phys2bids --help

Let's deal with some data!

Load in the first dataset and take a look.

phys2bids -in samefreq_multiscan.txt -out multiscan_info -info

Let's split the dataset into its functional scans!

phys2bids -in samefreq_multiscan.txt -out multiscan_split -ntp 534 513 -tr 1.2

Next, let's go all the way and bids-ify the data using the heuristic file!

phys2bids -in samefreq_multiscan.txt -out multiscan_bids -ntp 534 513 -tr 1.2 -sub 001 -ses 01 -heur heur_tutorial.py

Now, look at our next dataset.

phys2bids -in multifreq.acq -out multifreq_info -info

If we bids-ify the data, it will automatically be split into files for each frequency.

Here, I'm selecting only the first four channels, since it looks like the C02 and O2 channels weren't used to collect data for this recording.

phys2bids -in multifreq.acq -out multifreq_bids -ntp 60 -tr 1.5 -chsel 1 2 3 4 -sub 002 -ses 01 -heur heur_tutorial.py