Sarah Sheldon
Jon Kuziek
Kyle Mathewson
Attention Perception and Performance Lab
Universiy of Alberta
some python brain vis tools: http://visbrain.org/auto_examples/index.html
https://nistats.github.io/auto_examples/index.html#first-level-analysis-examples
https://github.com/neurolib-dev/neurolib
aim to use fNIRS tools already in MNE, https://mne.tools/dev/auto_tutorials/preprocessing/plot_70_fnirs_processing.html
plan is to load into pandas DataFrame and from there into MNE raw format
Example MNE loading with other NIRS data: https://github.com/mne-tools/mne-python/blob/master/mne/io/nirx/nirx.py
Optical imaging workflow currently, including hardware output data format: http://sites.psych.ualberta.ca/kylemathewson/optical-imaging/
Preprocessing routines currently in PPOD (matlab): Link unknown
Creation of electrode locations and source detector files in NOMAD (matlab): https://github.com/kylemath/nomad
Coregistration of optical locations on structural MRI in COREG (matlab): Link unknown
Matlab optical reconstruction of average data in MOPT3d (matlab) or OPT3d (fortran): https://github.com/kylemath/mopt3d
Install python3 then run in terminal or git Bash:
git clone https://github.com/kylemath/pyoptical
python3 -m venv venv
source venv/bin/activate
pip install --upgrade pip
pip install -r requirements.text
Then you can run the run test.py script by typing:
python test.py
or open the notebook by typing
jupyter notebook
and opening the .ipynb file
Make a branch of the master git repo to make any changes by:
git branch newBranchName
git checkout newBranchName
Check branch you are on and any changes to your branch
git status
Add file or all changes to a commit
git add filename.txt
or
git add .
Commit your added changes to your branch repo
git commit -m 'a message about what changed'
Push you branch changes to the github repo (the first time it asks you to type something extra first
git push
# clone a repo from github on your machine
# see newPyProj.sh for how to setup or see projects readme
git clone https://github.com/kylemath/pyoptical
# check what branch you are in and if files have changed
git status
# create new branch
git branch branchName
# move into another branch (need to save changes first)
git checkout master
git checkout branchName
git checkout -b branchName
# once branch changed add files to commit changes either one at a time or all changes (.)
git add file.name
git add .
# commit all those files you added and add a message of what you did
git commit -m "changes were made"
# push the commit to the remote repo (github.com)
git push
# pull any new changes from the remote repo (github.com)
git pull
# revert changes you don't like in a branch to the original file before you changed it
git checkout file.name
git checkout .Suggest we add changes in your branch to the master: Got to github.com/kylemath/pyoptical after doing the above steps click on make pull request add in information about changes and click make pull request then I review your changes or vice versa