Jim 10 User Manual

Home

  • Main xinapse.com web site
  • Overview
  • Quick start
  • New features
  • PDF manual
  • Usage terms

Hardware

  • Overview
  • Windows
  • Mac
  • Linux
  • Other

Installation

  • Introduction
  • Windows
    • Installing under Windows
    • Customising a Windows installation
  • Apple Mac
    • Installing on an Apple Mac
    • Customisng a Mac installation
  • Linux
    • Installing on a Linux system
    • Customising a Unix installation
  • Further steps for running Jim with a dongle
  • Setting up a license server
  • Setting up a license client
  • Installed help pages
  • Re-installing previous versions
    • Re-install Jim 9.0
    • Re-install Jim 8.0
    • Re-install Jim 7.0
    • Re-install Jim 6.0

Getting Started

  • Starting Jim
  • Window layout
  • FAQ

Handling Images

  • Loading images
  • Converting images
  • Converting raw data
  • Converting pictures
  • DICOM image management
  • DICOM query/retrieve
  • DICOM storage
    • Running the DICOM storage server
    • Setting up a stand-alone DICOM storage server
  • Saving images
  • Fast-save lists
  • DICOM send
  • Screen shots
  • Unloading & reloading images
  • Organising your images
  • Resampling images
  • Multi-planar reconstruction
  • Image anonymiser
  • Configuring DICOM Query/Retrieve
  • Configuring DICOM Send
  • Debugging DICOM issues

Display Controls

  • Introduction
  • Contrast
  • Layout
  • Paging
  • Zoom and pan
  • Colour mapping
  • Interpolation
  • Orthogonal views
  • Cross reference image
  • Image overlay
  • Complex display
  • Dimension display

Image Information

  • Descriptive info
  • Pixel intensities
  • Intensity profiles

Multiple Display

  • Spawning displays
  • Linking displays

Movie Display

  • Starting movie
  • Movie controls
  • Showing ROIs on movies
  • Exporting movies

Maximum Intensity Projection

  • Starting MIP
  • MIP options
  • Saving and exporting MIPs

3D Display

  • Introduction
  • General controls
  • Orthogonal planes
  • Iso-surfaces
  • Volume rendering
  • Rendering regions of interest
  • External 3D objects
  • Recording cines

Regions of Interest (ROIs)

  • Introduction
  • How ROIs look
  • Creating ROIs
  • Creating ROIs via a dialog
  • Editing ROIs
  • Advanced editing of Irregular ROIs
  • Annotating ROIs
  • Grouping ROIs
  • Saving and retrieving ROIs
  • ROI statistics
  • ROI intensities
  • ROI coordinates
  • ROI histograms & line profiles
  • The ROI totaliser
  • Masking with ROIs
  • Painting pixels
  • Audit trail
  • Roi Stats Format
  • Algorithms
  • Coordinates format
  • ROI intensities format

Image Algebra

  • Introduction
  • Input Images
  • The formula
  • Thresholds & limits
  • Image output
  • Algebra presets

Image fitting

  • Introduction
  • Using a built-in function
  • General least-squares
  • Speeding up fitting
  • Input images
  • Image output
  • Doing the fit
  • Saving to a preset
  • Roaming fit

Image synthesis

  • Introduction
  • Input images
  • Synthesis

Particle Analysis & Masking

  • Introduction
  • Intensity selection
  • Morphological operations
  • Particle connection
  • Particle editing
  • Applying particle analysis
  • Masking images

Fuzzy Connector

  • Introduction
  • Fuzzy connections
  • Algorithms

Brain Finder

  • Introduction
  • Outlining the brain
  • Calculating the BPF
  • Masking the brain

Defacing for Anonymisation

  • Introduction
  • Defacing

Brain Follow-Up

  • Introduction
  • Processing options
  • Image review

Brain Atrophy & Lesion Segmentation

  • Introduction
  • Processing options
  • Cross-sectional atrophy assessment
  • Longitudinal atrophy assessment
  • Cross-sectional atrophy with lesions
  • Longitudinal atrophy with lesions

Spinal Cord Atrophy

  • Introduction
  • Semi-automatic cord outlining
  • Quasi-automatic cord outlining
  • Semi-automatic cord follow-up
  • Quasi-automatic cord follow-up
  • Recommendations for best reproducibility

ROI Propagation

  • Introduction
  • Processing options
  • Distensibility calculation
  • Volume flow rate calculation
  • Pulse wave velocity calculation
  • Plugins

Cardiac Analysis

  • Introduction
  • Defing epi- and endo-cardial borders
  • Calculating segment intensities
  • Left ventricular function
  • Cardiac perfusion analysis
  • Cardiac strain analysis
  • Plugins

Brain Perfusion & DCE-MRI

  • Introduction
  • Brain perfusion
  • DCE-MRI
  • DCE-MRI plugins
  • Roaming intensities
  • AIF Resampler
  • Perfusion Algorithms

Quantitative susceptibility mapping

  • Introduction
  • Input images preparation
  • Unwrapping
  • Debackgrounding
  • Inversion

Dynamic Analysis

  • Introduction
  • Intensity selector
  • Arterial spin labelling
  • General linear model
  • Dynamic plugins
  • Roaming intensities

Fat/Water Separation

  • Introduction
  • Fat/water separation settings
  • Input images
  • Output images

CEST Analysis

  • Introduction
  • Input images
  • WASSR B0 estimation
  • Asymmetry analysis
  • Lorentzian fitting
  • pH estimation
  • Roaming intensities

Diffusion Tensor Analysis

  • Introduction
  • Gradient vectord and b-matrices
  • Setting the input images
  • Warp correction
  • Tensor analysis
  • Tractography

Image Registration

  • Introduction
  • Affine registration
  • Applying affine registration to other images
  • Time-seriess registration
  • Diffeomorphic registration
  • Applying diffeomorphic registration to other images

Uniformity (Bias Field) Correction

  • Introduction
  • Performing the correction
  • Apply the correction to other images

User Preferences & Properties

  • Introduction
  • Properties
  • General preferences
  • ROI preferences
  • Graph preferences

Keyboard Shortcuts & Drag-n-Drop

  • Keyboard shortcuts
  • Drag-and-drop

Task-based Help

  • Introduction
  • Lesion volumes - contouring method
  • Brain volumes
  • MTR histograms
  • Functional MRI (fMRI) analysis

Stand-alone Tools

  • Introduction
  • Tools with GUI and command-line interfaces
  • Tools with GUI interface only
  • Tools with command-line interface only
  • Usage messages
    • Asymmetry
    • Annot2Image
    • AutoCordFU
    • AutoCordFinder
    • AutoCrop
    • DicomSend
    • DiffeoRegister
    • Header
    • JimStats
    • LicensePing
    • LicenseServer
    • Lorentzianfitter
    • pHEhestimator
    • Props
    • QSMDebackground
    • QSMInvert
    • QSMUnwrap
    • Roi2Atlas
    • RoiTotals
    • Roivol
    • StorageServer
    • ToAnalyze
    • ToDicom
    • ToNIFTI1
    • ToNIFTI2
    • ToUNC
    • Tractography
    • WarpCorrection
    • WASSR

Programming Interface (API)

  • Writing your own programs
  • A.P.I. documentation
  • Programming examples
    • ExtractSlice
    • ImageHeader
    • ROIMask

Sample Images

  • Images for download

File Formats

  • ROI file format
  • Brain Finder log format
  • Totaliser log format
  • Graph data file
  • Image fit file
  • Affine transform file
  • Uniformity correction parameters
  • General linear model specification
  • Diffusion gradient specification Format
  • Fibre tracts format
  • Backus-Naur form

Bugs & Fixes

  • Bug Parade
  • Reporting bugs

Appendices

  • The file chooser
  • Patient and scan details
  • Input image masking options
  • Acknowledgements
Jim 10 User Manual
  • Stand-alone Tools
  • Tools with command-line interface only
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Tools with only a Command-Line Interface

The following have only a command-line interface:

  • Asymmetry
  • Annot2Image
  • AutoCordFU
  • AutoCordFinder
  • AutoCrop
  • DicomSend
  • DiffeoRegister
  • Header
  • JimStats
  • LicensePing
  • LicenseServer
  • Lorentzianfitter
  • pHEstimator
  • Props
  • QSMDebackground
  • QSMInvert
  • QSMUnwrap
  • Roi2Atlas
  • RoiTotals
  • Roivol
  • StorageServer
  • ToAnalyze
  • ToDicom
  • ToNIFTI1
  • ToNIFTI2
  • ToUNC
  • Tractography
  • WarpCorrection
  • WASSR

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