Contents

  • Introduction
    • Features overview
  • Notation and definition of terms
    • Notation
    • Definition of term
  • Tutorials
    • Loading an image
    • Viewing an image
    • Viewing multiple images
    • Using ROIs
    • Saving an image
  • Image Management
    • Loading and Sorting Images
    • Load and Image from your Hard Disk or Network
    • BOLD/DTI Wizard
    • DICOM database
      • Configuring the nordicICE database
    • DICOM Reader
    • NIFTI file manager
    • Saving Images
      • Copy Images and color bars
      • Save Data
        • Converting and Saving Siemens Mosaic Images
        • Saving Images in DICOM format
        • Editing the Image Header
        • Saving multi-dimensional data
        • Displaying ROI information on saved images
        • Saving ROI data
      • Saving images to the DICOM database
  • Image Viewing
    • The active image window
      • Scrolling
      • Sorting multi-dimensional datasets
      • Delete current image
      • Resize the active window
      • Zoom
      • Pan
      • Smooth
      • Zoom/Pan info
      • Image contrast/intensity
      • Active palette
      • Invert palette
      • Image information
      • Run movie
      • Series Descriptor
    • Linking multiple windows
  • Image processing
    • Image Arithmatic functions
      • Image arithmetics applied to a single dataset
      • Image Arithmetics based on two datasets
    • Multi-Planar Reformat (MPR) Window
      • MPR basics
      • Edit options
      • Navigation in MPR
      • Overlays in MPR
      • Navigation in MPR
      • Maximum Intensity Projection (MIP)
    • Co-registration
      • Inter-modality co-registration
      • Motion and eddy current correction
      • Motion correction
    • Image segmentation and masking (pixel edit)
  • Adaptive processing
    • Histogram equalization
    • Image Binarization
    • Median Filter
  • Working with image overlays
    • Load image overlays
    • Modify image overlays
    • Image co-registration from DICOM geometry paramters
  • Image Analysis
    • Line profile
    • Measure distance
    • Region of interest (ROI) Analysis
      • Draw and Measure Pixel Values in a Region of Interest (ROI)
      • Mirror ROIs around a reference line
      • Saving and loading ROIs
      • Copying and pasting ROIs
    • The ROI Buffer
      • Saving ROI data to the Buffer
      • ROI Buffer functions
      • Saving and Loading ROI Specifications
    • Advanced ROI functionality
      • ROI based image masking
      • Slice-dependent adjustments of the ROI mask
    • ROI intensity curves
      • ROI Intensity Curves for multi-dimensional datasets
      • Axis options.
    • ROI-based data modelling
      • Data modelling results
    • ROI Histogram
      • ROI Histogram options
  • Perfusion Analysis module
    • Perfusion analysis: step by step
      • Loading a dynamic dataset
      • Starting the perfusion module
      • Main settings
      • Pre-processing settings
      • Parameter settings
      • Arterial Input Function settings
    • Perfusion analysis options
    • Advanced perfusion analysis options
  • VAI (vessel architectural imaging) Analysis
    • Introduction
    • Theoretical background - Vessel Architectural Imaging
    • Getting started with VAI
    • VAI data interaction
    • Displaying data as volume/MIP reader
    • Complete VAI analysis workflow
      • Data format and image parameters
      • Coregistration of perfusion/structural series
      • Volume of interest and tumor segmentation
      • ADC map
      • Performing perfusion / VAI analysis
      • Visualizing parametric maps as overlays
      • Statistical output maps
    • Overview of menu options and shortcuts
    • Performing VAI analysis in batch mode
    • VAI spesific perfusion maps
    • References
  • Dynamic contrast enhanced (DCE) imaging Module
    • Theory
    • Starting the DCE analysis
    • Main menu
    • Pre-processing
    • Parameter specifications
    • Analysis options
    • AIF deconvolution
    • ROI Analysis
  • ASL Analysis
    • Process
    • Parameters
    • Quantitative analysis
  • Diffusion Analysis
    • DWI Introduction
    • DWI analysis
    • DTI (6 or more diffusion directions)
    • Fiber Tracking
  • BOLD Analysis module
    • Process BOLD Image Data
    • Output BOLD Image Data Analysis
    • Edit/Create Design File
    • Create Paradigm in Design File
    • Specify Contrast in Design File
    • Specify Processing Steps in Design File
    • Advanced Settings
  • Resting State fMRI Analysis
    • Seed-based fMRI resting state analysis
    • Pre-processing in resting state fMRI
  • Brain Extraction (Optional plugin module)
    • Introduction
    • Performing brain extraction
      • Configuring the brain extraction parameters
      • Running brain extraction
  • Relaxation Analysis
    • T2 / R2 relaxation analysis
    • T1 / R1 relaxation analysis
  • Batch analysis
    • Getting started
    • Batch perfusion analysis
    • Pre-process
    • Batch DCE analysis
    • Batch - ASL Analysis
    • FreeSurfer -segmentation extraction
    • ROI analysis in batch
    • Batch Coregistration
  • Co-registration
    • Inter-modality co-registration
  • Reference for Dialog Boxes
    • Arithmetic Analysis Settings
      • Arithmetic operation tab
      • Drag & Drop tab
      • Pre process tab
    • Axis options
    • Brain Extraction Configuration
    • BOLD/DTI Wizard
      • BOLD/DTI Wizard - Select Series
      • BOLD/DTI Wizard - DTI Settings
      • BOLD/DTI Wizard - BOLD Settings
      • BOLD/DTI Wizard - Summary
    • Change image intensity / contrast
    • DICOM Edit
    • DICOM Dump
    • DICOM Reader
    • Diffusion Analysis
      • Diffusion Weighted Imaging (DWI) tab
      • Diffusion Tensor Imaging tab
      • DTI interaction panel
    • BOLD interaction panel
    • Dicom DB import
    • DTI Gradient Configuration
    • Dynamic scan-time values
    • Echo time (TE) values
    • Edit fields
    • Export settings
    • Gaussian Smoothing
    • Image Histogram
    • Image Histogram Options
    • Image Zoom / Pan
    • Inversion time (TI) values
    • Load multi-ROI (ROI buffer) file
    • Load ROI/SEG file
    • Make Mask
    • Movie
    • Multi-Planar Reformat (MPR)
    • Co-registration
      • Coregistration Panel
    • nordicICE Database
      • Database tab
      • Query/Retrieve tab
      • Settings tab
      • Transfer Log tab
    • Database validation
      • Database validation
      • Database validation - start integrity validation
      • Database validation - start image link validation
      • Database validation - check/remove invalid image links
    • Open
    • Overlay settings
    • ROI Buffer
    • ROI from Grayscale Segmentation
    • ROI Intensity Curves
      • T1 Relaxation tab
      • T2 Relaxation tab
      • Gamma variate tab
      • Kinetic modelling tab
      • Linear tab
      • Preprocess tab
    • ROI statistics
    • Save
    • Save all images
    • Save ROI Buffer
    • Save ROI Position
    • Save value buffer
    • Select remote entity
    • Settings
      • Image Save tab
      • Image Formats tab
      • Various tab
      • Image Linking tab
      • Win L/W Presets tab
      • Multi-Planar Reformat tab
    • Nifti File Manager
    • T1 relaxation analysis setting
      • Sequence specifications tab
      • Pre-process and ansalysis tab
      • Output tab
    • T2 relaxation analysis setting
      • Sequence specifications tab
      • Pre-process and ansalysis tab
      • Output tab
  • Using nordicICE Menus
    • File Menu
    • Edit Menu
    • Modify Menu
    • View Menu
    • Measure Menu
    • Process Menu
    • Modules Menu
    • Options Menu
    • Window Menu
  • Using nICE Toolbars
    • Data managment tools
    • Image edit tools
    • Image measurement tools
    • Image visualization tools
    • Image processing tools
  • Credits
    • VTK - The Visualization Toolkit