Menubar

• File (File menu)

• Functions (Functions menu)

• Registration (Registration menu)

• Segmentation (Segmentation menu)

• Mapping (Mapping menu)

• Diffusion (Diffusion menu)

• Views

• Window (Window menu)

• Keyboard Shortcuts

File

• Open…

• Open template

• Open from format >

  • Open Nifti…

  • Open Nrrd…

  • Open Minc…

  • Open FreeSurfer MGH…

  • Open Sisyphe…

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  • Open VTK…

• Recent files

• Open user folder

• Save

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• Save to format >

  • Save Nifti…

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  • Save Nrrd…

  • Save Minc…

  • Save VTK…

• Close

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• Preferences…

• Download manager…

• Check for update…

• Edit attributes…

• ID replacement…

• Anomynize…

• Edit volume labels…

• ROIs to label volume…

• Volumes to label volume…

• Label volume to ROIs…

• Label volume to mask…

• Remap label volume…

• Import >

  • Import Nifti…

  • Import Minc…

  • Import Nrrd…

  • Import Vtk…

  • Import Sisyphe (*.vol)…

• Export >

  • Export Nifti…

  • Export Minc…

  • Export Nrrd..

  • Export Vtk…

  • Export Numpy…

• DICOM >

  • DICOM import…

  • DICOM RT import…

  • DICOM export…

  • DICOM Query/Retrieve from DICOM SCP Server…

  • DICOM Dataset…

  • Xml DICOM attributes…

• Edit LUT…

• Quit…

Functions

• Join single component volume(s)

• Split multi component volume(s)

• Flip axis…

• Permute axis…

• Remove neck slilces…

• Datatype conversion…

• Attributes conversion…

• Filters >

  • Mean…

  • Median…

  • Gaussian…

  • Gradient magnitude…

  • Laplacian…

  • Anistropic diffusion…

• Intensity processing >

  • Histogram intensity matching…

  • Regression intensity matching…

  • Intensity normalization…

• Texture feature maps…

• ROI texture features…

• Bias field correction…

• Atlas labeling >

  • ROI(s) atlas labeling…

  • Mesh(es) atlas labeling…

  • Tool(s) atlas labeling…

• Voxel-by-voxel processing >

  • Mean volume…

  • Median volume…

  • Standard deviation volume…

  • Minimum volume…

  • Maximum volume…

  • Algebra…

• Processing workflow…

• Workflows

• Install plugin…

• Remove plugin…

• Plugins

Registration

• Stereotactic frame detection…

• AC-PC selection…

• Volume reorientation…

• Manual registration…

• Rigid registration…

• Affine registration…

• Displacement field registration…

• ICBM normalization…

• Batch registration…

• Time series realignment…

• Eddy current correction…

• Resample…

• Asymmetry displacement field…

• Displacement field jacobian determinant…

Segmentation

• KMeans clustering…

• KMeans segmentation…

• Skull striping…

• Tissue segmentation…

• Cortical thickness…

• Registration based segmentation…

• Structs

• Deep learning segmentation >

  • Atlas parcellation…

  • Focal cortical dysplasia detection…

  • Hippocampus segmentation…

  • Hypo-intensity lesion segmentation…

  • Medial temporal clustering…

  • Metastasis segmentation…

  • Microbleeds segmentation…

  • Tissue segmentation…

  • Tumor clustering…

  • White matter hyper-intensities segmentation…

Mapping

• Model >

  • fMRI conditions…

  • fMRI subjects/conditions…

  • fMRI groups/subjects/conditions…

  • One sample t-test…

  • Two sample t-test…

  • Paired t-test…

  • ANCOVA…

  • GLM subjects/conditions…

  • GLM groups/subjects/conditions…

  • GLM groups…

  • GLM groups/subjects…

  • Models >

• Contrast…

• Result…

• Laterality index…

• Conjunction…

• t to z-map conversion…

• Time series preprocessing…

• Seed-to-voxel time series correlation…

• Single-subject time series ICA…

• Time series correlation matrix…

• Quantitative MR maps >

  • B0 map…

  • B1 map…

  • T1 map…

  • T2 map…

  • T2’ map…

  • MTR map…

  • QSM map…

• ASL perfusion…

• Dynamic suceptibility contrast…

Diffusion

• Gradients…

• Preprocessing…

• Diffusion model…

• Diffusion analysis along perivascular space…

• Tractogram generation…

• Bundle >

  • ROI based streamlines selection…

  • Filter based streamlines selection…

  • Template based streamlines selection…

  • Density map…

  • Path length map…

  • Connectivity matrix…

Views

• Slice view >

• Orthogonal view >

• Synchronize view >

• Projection view >

• Multi-component view >

• Database >

• Screenshots >

• IPython >

Window

• About…

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Keyboard Shortcuts

• CTRL O Open…

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• CTRL ? Edit attributes…

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• F1 Slice view

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• F4 Projection view

• F5 Multi-component view

• F6 Database

• F7 File browser

• F8 Screenshots

• F9 IPython

• F11 Full screen