micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
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Updated
Apr 16, 2024 - Shell
micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
Gray-matter Based Spatial Statistics
Generate a package-manager-friendly mouse brain atlases collection.
3D print your brain from a T1 MRI image using Docker.
Ironsmith is a comprehensive, fully automated pipeline for creating and processing Quantitative Susceptibility Maps (QSM), extracting QSM based iron concentrations from subcortical and cortical brain regions and evaluating the quality of QSM data using SNR measures and assessment of outlier regions on phase images.
atlasBREX: Automated averaged template-derived brain extraction in animal MRI
Scripts for MRI preprocessing
Musiré – Multimodal simulation & reconstruction framework for the radiological imaging sciences
runs fast optimization of preprocessing pipelines for BOLD fMRI
Run the recommended preprocessing procedure provided by mrtrix3. The options available mostly reflect the optimal DESIGNER pipeline that was recently proposed. This App runs for >15 on topup if both PA and AP dwi files are provided. It detects bvecs flipping (dwigradcheck) and update the gradient table accordingly.
Anonymization of freesurfer output based on metadata dropping and defacing.
Scripts related to "White Matter Microstructure in Attention-Deficit/Hyperactivity Disorder: A Systematic Tractography Study in 654 Individuals"
Freesurfer processing for 3D brain printing
Pipeline and tools to preprocess MR data
Scripts related to "Associations between attention-deficit hyperactivity disorder (ADHD) symptom remission and white matter microstructure: A longitudinal analysis"
SVRTK packaged as a MONAI Application Package (MAP), including for deployment on AIDE
Dockerfile to create a docker image containing open source mritools for data handling, reconstruction and post-processing
Add a description, image, and links to the mri topic page so that developers can more easily learn about it.
To associate your repository with the mri topic, visit your repo's landing page and select "manage topics."