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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.

!!! info "New release: Clinica 0.2!" We are very pleased to announce the release 0.2 of Clinica. The release notes are available here: v0.2.0, v0.2.1.

• Installation
• Third-party software

User documentation

Clinica environment

• Interacting with Clinica
• BIDS: the input raw data structure
• CAPS: the processed data structure

Pipelines (clinica run)

• Anatomical MRI (T1-weighted)
  • t1-volume - Processing of T1w MR images using SPM: tissue segmentation and spatial normalization
  • t1-freesurfer - Processing of T1w MR images using FreeSurfer: cortical surface, subcortical structures and volumetrics
• Diffusion MRI (DWI)
  • dwi-preprocessing-* - DWI pre-processing: correction of head motion, magnetic susceptibility, eddy current and bias field induced distortions
  • dwi-dti - DTI scalar maps (FA, MD, AD, RD) and spatial normalization: extraction of DTI-based measures (FA, MD, AD, RD)
• Functional MRI (fMRI)
  • fmri-preprocessing - fMRI pre-processing: slice timing and motion correction, brain extraction, and spatial normalization
• PET
  • pet-volume - Volume-based processing of PET images: registration to T1w MRI, intensity normalization, partial volume correction and spatial normalization
  • pet-surface - Surface-based processing of PET images: projection of the PET signal onto the subject’s cortical surface
• Statistics
  • statistics-surface - Surface-based mass-univariate analysis with SurfStat
• Machine Learning
  • machinelearning-prepare-spatial-svm Prepare input data for spatially regularized SVM
  • Classification based on machine learning

Dataset converters (clinica convert)

• Online neuroimaging databases (ADNI, AIBL, OASIS) to BIDS converters

I/O tools (clinica iotools)

• Data handling tools for BIDS and CAPS compliant datasets

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

• Report an issue on GitLab
• Use the Clinica Google Group to ask for help!

License

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

Citing Clinica

For publications or communications using Clinica, please include the following text:

!!! quote "Citing Clinica" Analyses were performed using the Clinica software platform (www.clinica.run) developed by the ARAMIS Lab (www.aramislab.fr).

Each pipeline's page includes text to cite the software packages that are used by Clinica. Use them depending on the specific pipelines that you used (for example, citing SPM when using the t1-volume pipeline).

!!! info "Disclaimer" Clinica is a software for research studies. It is not intended for use in medical routine

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