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
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.
KUL/UZ NeuroImaging Suite. A set of tools for brain and spine MRI analysis.
Scripts for MRI preprocessing
Data and tools from the publication "Evolution of Cortical Geometry and its Link to Function, Behaviour and Ecology" by Schwartz et al. for mapping values defined on cortical surfaces between species based on their phylogenetic relationship
Peak width of Skeletonized Mean Diffusivity (PSMD)
Shell scripts to run FreeSurfer's recon-all in parallel on multi-core machines.
A modified FSL version for use with Slurm
General utility scripts, documentation, and analysis tutorials for Smith Lab.
A sample neuroimaging pipeline for the fMRI data collected by the Aging Brain Cohort.
A simple and intuitive wrapper for FSL tools.
brainlife app - runs AFNI's skullstrip function on NIfTI files
Common Docker Image for the Dosenbach and Greene Labs
Preprocessing pipeline for region of interest selection, linear and non-linear registrations, ICA-based noise rejection, spatial smoothing, and more.
Pipeline computing volumes statistics for different brain lobes according to a atlas.
Repository containing files associated with ENIGMA diffusion weighted image preprocessing protocol and instructional video series. Designed by Ryan Cali for the 2022 ReproNim Fellowship Project and the Imaging Genetics Center at the University of Southern California. Questions? Reach out to the author: rcali@loni.usc.edu
Preprocessing files for EuskalIBUR
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