Clinica Documentation¶
What is Clinica ?¶
Clinica is a software platform for clinical neuroscience research studies using multimodal data and most often longitudinal follow-up. You can learn more on this page.
Installation¶
Clinica can be installed on MacOS 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 using the command line.
User documentation¶
Clinica environment¶
Pipelines (clinica run
)¶
-
Anatomical MRI
t1-linear
- Linear processing of T1w MR images: affine registration to the MNI standard space of T1 imagesflair-linear
- Linear processing of FLAIR images: affine registration to the MNI standard space of FLAIR imagest1-volume
- Processing of T1w MR images using SPM: tissue segmentation and spatial normalizationt1-freesurfer
- Processing of T1w MR images using FreeSurfer: cortical surface, subcortical structures and volumetricst1-freesurfer-longitudinal
- Longitudinal 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 distortionsdwi-dti
- DTI scalar maps (FA, MD, AD, RD) and spatial normalization: extraction of DTI-based measures (FA, MD, AD, RD)dwi-connectome
- Construction of structural connectome: computation of fiber orientation distributions, tractogram and connectome
-
PET
- Introduction to concepts used in the PET pipelines: partial volume correction and standardized uptake value ratio (SUVR) map computation
pet-linear
- Linear processing of PET images: affine registration to the MNI standard space and intensity normalizationpet-volume
- Volume-based processing of PET images: registration to T1w MRI, intensity normalization, partial volume correction and spatial normalizationpet-surface
- Surface-based processing of PET images: projection of the PET signal onto the subject’s cortical surfacepet-surface-longitudinal
- Surface-based longitudinal processing of PET images: projection of the PET signal onto the subject’s cortical surface
-
Statistics
statistics-surface
- Surface-based mass-univariate analysis with SurfStatstatistics-volume
- Volume-based mass-univariate analysis with SPM
-
Machine Learning
machinelearning-prepare-spatial-svm
- Prepare input data for spatially regularized SVMmachinelearning-classification
- Classification based on machine learning
-
Deep learning
- You can use the ClinicaDL framework for the reproducible processing of neuroimaging data with deep learning methods.
Dataset converters (clinica convert
)¶
Clinica provides tools to curate several publicly available neuroimaging datasets and convert them to BIDS namely:
adni-to-bids
- ADNI: Alzheimer’s Disease Neuroimaging Initiativeaibl-to-bids
- AIBL: Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageinggenfi-to-bids
- GENFI:Genetic Frontotemporal dementia Initiativehabs-to-bids
- HABS: Harvard Aging Brain Studyixi-to-bids
- IXI: Information eXtraction from Imagesnifd-to-bids
- NIFD: Neuroimaging in Frontotemporal Dementiaoasis-to-bids
- OASIS: Open Access Series of Imaging Studiesoasis3-to-bids
- OASIS-3: Longitudinal Neuroimaging, Clinical, and Cognitive Dataset for Normal Aging and Alzheimer’s Diseaseukb-to-bids
- UK Biobank: Large-scale biomedical database and research resource in the United Kingdom
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¶
- Check for past answers in the old Clinica Google Group
- Start a discussion on GitHub
- Report an issue on GitHub
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., 2021]
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.
Contact us !¶
- Check for past answers on Clinica Google Group
- Start a discussion on GitHub
- Report an issue on Github