Tools with GUI interface only - Jim 10 User Manual

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

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

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 GUI interface only

Previous Next

Tools with only a GUI Interface

The following have only a graphical (GUI) interface:

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Jim3D
JMovie
MIP
QueryRetrieve

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