PySisyphe documentation

Contents:

• PySisyphe documentation
• Overview
• Installation
  • From binary installer
  • From source
• Main window
• Toolbar
• Thumbnail bar
  • Thumbnails
  • Popup menu
  • LUT widget
  • Overlay widget
• Widgets
  • Single file selection
  • Multiple file selection
  • Thresholding
• Slice view widget
  • Controls
  • Icon bar
  • Popup menu
• Orthogonal view widget
  • Controls
  • Icon bar
  • Transfer function widget
  • Popup menu
• Synchronized view widget
  • Controls
  • Icon bar
  • Popup menu
• Projection view widget
  • Controls
  • Icon bar
  • Popup menu
• Multi-component view widget
  • Controls:
  • Icon bar
  • Popup menu
• Database Manager
• Screenshots manager
• IPython console
  • Most popular commands
• ROI tab of the dock
  • ROI list
  • ROI item
  • Icon bar
  • Set Operators
• ROI Tools tab of the dock
  • Brush
  • Slice tools
  • Slice blob tools
  • Volume tools
  • Volume blob tools
  • Brush settings
  • Statistics dialog box
• Mesh tab of the dock
  • Mesh list
  • Mesh item
  • Icon bar
  • Mesh tools
  • Mesh settings
• Target/Trajectory tab of the dock
  • Target/Trajectory list
  • Target/Trajectory item
• Tracking tab of the dock
  • Whole tractogram virtual dissection tools
  • Bundle list
  • Bundle item
• Documentation tab of the dock
• Menubar
  • File
  • Functions
  • Registration
  • Segmentation
  • Mapping
  • Diffusion
  • Views
  • Window
• File menu
  • Open
  • Open template
  • Open from format
  • Open recent
  • Open user folder
  • Save
  • Save all
  • Save as
  • Save to format
  • Close
  • Close all
  • Preferences
  • Download manager
  • Check for update
  • Edit attributes
  • ID replacement
  • Anonymize
  • Edit volume labels
  • ROIs to label volume
  • Volumes to label volume
  • Label volume to ROIs
  • Label volume to mask
  • Remap label volume
  • Import
  • Export
  • Dicom import
  • Dicom RT import
  • Dicom export
  • Dicom query/retrieve from Dicom SCP Server
  • Dicom dataset
  • XML Dicom attributes
  • Edit LUT
  • Quit
• Functions menu
  • Join single component volume(s)
  • Split multi component volume(s)
  • Flip axis
  • Permute axis
  • Remove neck slices
  • Datatype conversion
  • Attributes conversion
  • Mean filter
  • Median filter
  • Gaussian filter
  • Gradient magnitude filter
  • Laplacian filter
  • Anisotropic diffusion filter
  • Histogram intensity matching
  • Regression intensity matching
  • Intensity normalization
  • Texture feature maps
  • ROI Texture features
  • Bias field correction
  • Mean volume
  • Median volume
  • Standard deviation volume
  • Minimum volume
  • Maximum volume
  • Algebra
  • Workflow processing
  • Workflows
  • Install plugin
  • Remove plugin
  • Plugins
• Registration menu
  • Stereotactic frame detection
  • AC-PC selection
  • Volume reorientation
  • Manual registration
  • Rigid registration
  • Affine registration
  • Displacement field registration
  • ICBM spatial normalization
  • Batch registration
  • Time series realignment
  • Eddy current correction
  • Resample
  • Asymmetry displacement field
  • Displacement field jacobian determinant
• Segmentation menu
  • KMeans clustering
  • KMeans segmentation
  • Skull stripping
  • Mixture model tissue segmentation
  • Cortical thickness
  • Registration based segmentation
  • Structs
  • Deep-learning Hippocampus segmentation
  • Deep-learning Hypo-intensity lesion segmentation
  • Deep-learning Medial temporal segmentation
  • Deep-learning Tissue segmenation
  • Deep-learning Tumor clustering
  • Deep-learning White matter hyper-intensities segmentation
• Mapping menu
  • fMRI model definition
  • General linear model definition
  • 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
  • Dynamic susceptibility contrast
• Diffusion menu
  • Gradients
  • Preprocessing
  • Diffusion model
  • tractogram generation
  • ROI based streamlines selection
  • Filter based streamlines selection
  • Template based streamlines selection
  • Density map
  • Path length map
  • Connectivity matrix
• Window menu
  • About
  • Minimize
  • Maximize
  • Full screen
  • Show/Hide Toolbar
  • Show/Hide Thumbnail
  • Show/Hide Dock
  • Show/Hide Status bar
  • Next tab
  • Previous tab
  • Slice view
  • Orthogonal view
  • Synchronized view
  • Projection view
  • Multi-component view
  • Database
  • Screenshots
  • IPython
• Core API
  • Packages
  • Sisyphe.core.sisypheConstants
  • Sisyphe.core.sisypheDatabase
  • Sisyphe.core.sisypheDicom
  • Sisyphe.core.sisypheDownload
  • Sisyphe.core.sisypheFiducialBox
  • Sisyphe.core.sisypheImage
  • Sisyphe.core.sisypheImageAttributes
  • Sisyphe.core.sisypheImageIO
  • Sisyphe.core.sisypheLUT
  • Sisyphe.core.sisypheMesh
  • Sisyphe.core.sisypheMeshIO
  • Sisyphe.core.sisypheRecent
  • Sisyphe.core.sisypheROI
  • Sisyphe.core.sisypheSettings
  • Sisyphe.core.sisypheSheet
  • Sisyphe.core.sisypheStatistics
  • Sisyphe.core.sisypheTools
  • Sisyphe.core.sisypheTracts
  • Sisyphe.core.sisypheTransform
  • Sisyphe.core.sisypheVolume
  • Sisyphe.core.sisypheXml
• Widgets & dialogs API
  • Understanding view widgets
  • Single viewport widgets
  • Multiple viewport widgets
  • Icon bar widgets
  • LUT widgets
  • Select file(s) widgets
  • Settings widgets
  • Generic results dialog
  • Progress & wait dialog
• License
• Contact
  • Affiliations
• Version history
  • Version increment rules
  • version 0.9.1, build 26/07/2025
  • version 0.12.9, build 05/08/2025
  • version 0.12.11, build 28/08/2025
  • version 0.12.16, build 30/08/2025
  • version 0.16.5, build 13/10/2025
  • version 0.18.3, build 16/10/2025
  • version 0.18.9, build 01/11/2025

Indices and tables

• Index

• Module Index

• Search Page