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SlicerNeuro

Extension for 3D Slicer than installs tools commonly needed for neuroimaging, besides providing two extra modules.

Modules

  • ACPC Transform: Calculate a transformation that aligns brain images to Talairach coordinate system (also known as stereotaxic or ACPC coordinate system) based on anatomical landmarks.
  • ImportGifti: Loads gifti files from a BIDS directory to 3D Slicer and saves them as vtk files in a specified output folder. These files can be reloaded to 3D Slicer.

Extensions

The extension automatically installs these commonly used extensions: SlicerFreeSurfer, SlicerDcm2nii, SlicerDMRI, SlicerWMA, UKFTractography, HDBrainExtraction, SwissSkullStripper.

Other neuroimaging related extensions that users need to install manually: T1Mapping, T2mapping, T1_ECVMapping, DTIPrep, DTIProcess, DTI-Reg, DTIAtlasBuilder, DTIAtlasFiberAnalyzer, DiffusionQC, SlicerNeuroSegmentation, Stereotaxia, SkullStripper, BrainVolumeRefinement, SlicerNetstim.