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Clinica Documentation

What is Clinica?

Installation

Clinica can be installed on Mac OS X and Linux (CentOS or Debian/Ubuntu) machines, and possibly on Windows computers with a Linux Virtual Machine. We assume that users installing and using Clinica are comfortable with using the command line.

User documentation

Clinica environment

Pipelines (clinica run)

Dataset converters (clinica convert)

Clinica provides tools to curate several publicly available neuroimaging datasets and convert them to BIDS namely:

Note

We provide converters for the datasets used in the Aramis Lab. Feel free to contact us if you are interested in another dataset or to contribute!

I/O tools (clinica iotools)

Visualize pipeline outputs (clinica visualize)

Clinica allows visualization of the main outputs of some pipelines. Currently only supported for the t1-freesurfer pipeline.

Clinica at conferences

Find on this page the presentations and demo materials used when we showcase Clinica.

Support

License

Clinica is distributed under the terms of the MIT license given here.

Citing Clinica

For publications or communications using Clinica, please cite [Routier et al] as well as the references mentioned on the wiki page of the pipelines you used. Each page includes text to cite the software packages that are used by Clinica (for example, citing SPM when using the t1-volume pipeline).

Disclaimer

Clinica is a software for research studies. It is not intended for use in medical routine.


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