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
KUL/UZ NeuroImaging Suite. A set of tools for brain and spine MRI analysis.
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.
General utility scripts, documentation, and analysis tutorials for Smith Lab.
A modified FSL version for use with Slurm
Scripts for MRI preprocessing
Shell scripts to run FreeSurfer's recon-all in parallel on multi-core machines.
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
Preprocessing files for EuskalIBUR
runs AFNI's 3dQwarp function over a NIfTI file
An API to interactively run the 3D reconstruction software PyReconstruct on the Lonestar6 supercomputer.
Preprocessing pipeline for region of interest selection, linear and non-linear registrations, ICA-based noise rejection, spatial smoothing, and more.
An API to interactively run the AlignEM-SWiFT NG v0.3.5 software on the Lonestar6 supercomputer.
A simple and intuitive wrapper for FSL tools.
A tool for automatically segmenting white matter lesions on human brain MRI images
Scripts and pipeline for the handling of scripts from DICOMS to 4DFP and then analysis.
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