Package: phys2cvr
phys2cvrA python-based tool to generate regressor for and/or estimate CVR maps and their lag.The project is currently under development stage alpha.
Any suggestion/bug report is welcome! Feel free to open an issue.This project follows theall-contributorsspecification. Contributions of any kind welcome!DocumentationFull documentation coming soon!CiteIf you usephys2cvrin your work, please cite either the all-time Zenodo DOIor the Zenodo DOI related to the version you are using.
Please cite the following paper(s) too:Moia, S., Stickland, R. C., Ayyagari, A., Termenon, M., Caballero-Gaudes, C., & Bright, M. G. (2020). Voxelwise optimization of hemodynamic lags to improve regional CVR estimates in breath-hold fMRI. In 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC) (pp. 1489–1492). Montreal, QC, Canada: IEEE.https://doi.org/10.1109/EMBC44109.2020.9176225If you are using the--brightspinconfiguration option:Moia, S., Termenon, M., Uruñuela, E., Chen, G., Stickland, R. C., Bright, M. G., & Caballero-Gaudes, C. (2021). ICA-based denoising strategies in breath-hold induced cerebrovascular reactivity mapping with multi echo BOLD fMRI. NeuroImage, 233, 117914.https://doi.org/10.1016/j.neuroimage.2021.117914If you are using the--brightspin-clinicalconfiguration option:Stickland, R. C., Zvolanek, K. M., Moia, S., Ayyagari, A., & Bright, M. G. (2021). A practical modification to a resting state fMRI protocol for improved characterization of cerebrovascular function. Supplementary Material. Neuroimage.If you are using the--baltimore-lagconfiguration option:Liu, P., Li, Y., Pinho, M., Park, D. C., Welch, B. G., & Lu, H. (2017). Cerebrovascular reactivity mapping without gas challenges. NeuroImage, 146(November 2016), 320–326.https://doi.org/10.1016/j.neuroimage.2016.11.054If you are using the--baltimoreconfiguration option, please cite only the Zenodo DOI and the last listed paper.InstallationInstall on any*nixsystem using python and pip, or clone this repository and install locally (run setup.py or pip).phys2cvrsupports python versions 3.6+. However, please note that no tests are currently run.Install withpip(recommended):exclamation::exclamation::exclamation: Please note that some systems might require to usepip3instead ofpip.Basic installation:For basic installation, simply run:pipinstallphys2cvrClone from Github / install withoutpip:exclamation::exclamation::exclamation: Please note thatphys2cvris continuously deployed, i.e. the latest feature available are immediately released on PyPI.
To installphys2cvrfrom Github, clone the repository first, then move to the cloned folder and run:pythonsetup.pyinstallAlternatively,pipcan be used too:pipinstall.Developer installationTo be sure you have everything installed to develop (and test)phys2cvr,forksmoia/phys2cvrto your repository, then clone it locally and move inside the cloned folder. Finally, run the following commands from within the repository main folder:# Add upstream remotegitremoteaddupstreamgit@github.com:smoia/phys2cvr.git# Fetch everything, tags includedgitfetch--all--tags# Checkout master (the main development branch) and make it track upstreamgitcheckoutmaster
gitbranch--set-upstream-to=upstream/master# !!! VERY IMPORTANT !!!# Set the default push to origin, in order NOT to push by mistake to upstream.gitconfigremote.pushDefaultorigin# Install package with pip using the developer mode and the `[dev]` label# You might need to use pip3 depending on how you set up your systempipinstall-e.[dev]If you make changes that you consider fundamental/interesting for the whole community, feel free to open a PR!Run/usephys2cvrYou can run thephys2cvrworkflow in a shell session (or in your code) - just follow the help:phys2cvr--helpAlternatively, you can use phys2cvr as a module in a python session (or within your python script):importphys2cvrasp2cp2c.__version__Full API coming soon.Contributors ✨Thanks goes to these wonderful people (emoji key):Stefano Moia💻🤔🚇📆Kristina Zvolanek💻🐛Andrew Vigotsky💻LicenseCopyright 2021, Stefano Moia.Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.