• PMOD Base Functionality Introduction
• Starting PMOD 
  • PMOD Docked Interface
  • PMOD ToolBox Interface (Legacy)
• PMOD Basics
  • Directory Tree
  • Basic User Interface Elements
  • Keyboard Shortcuts
  • Problem Reporting
• PMOD Unified Data Loader
  • DATABASE Page
  • DICOM Page
  • AUTODETECT Page
• General Configuration
  • USERS
    • User Creation
    • USER SETTINGS
      • User-Specific Database Preferences
      • STATISTICS
      • PRESETS
    • PXMOD, PKIN, READ/WRITE, LOADING, Color Tables Plug-ins
    • MODULES
  • DCM DICOM Functionality
    • NODEs [C-STORE, Q/R]: DICOM Client Configuration
    • DICOM SERVER Configuration
      • DICOM Server Properties
      • Multiple DICOM Server Creation
      • What happens with received DICOM Images
      • Incoming Folder
      • DICOM Server Starting
      • Implementation of DICOM Servers on a Dedicated Machine
    • DICOM Special Cases
    • DICOM Advanced Options
    • DICOM Query/Retrieve
    • DICOM Query Loader (Auxiliary Server)
  • DATABASE Functionality
    • Creation and Configuration of Databases
    • Setting up a Transaction Server to Publish a Database
    • Loading Data from Databases
      • Image Data Loading
      • Component Data Loading
    • Saving Data to Databases
      • Image Data Saving
      • Component Data Saving
    • Exporting Data from Databases
      • Image Data Export
      • Component Data Export
    • Data Association
      • Image Association
      • VOI Association
      • Curve Association
      • Automatic Association
      • Inspecting Associations
    • Administrative Tools
      • Database Administration
      • Export of Database Contents
      • Replication from one Database to Another
      • External Backup Procedure
      • Aggregation of Components such as VOIs and Kinetic Parameters
  • On Start
• PMOD Server Administration
• Tool Configurations
• Data Loading and Saving
  • Image Data Formats
    • Format Overview
    • Format Descriptions
  • Image Data Loading
    • Data Units
    • Database Loading
    • DICOM Loading
    • File-based loading
    • Loading Macros
    • Buffer Loading
  • Image Data Transformations during Loading
    • Changing the Image Orientation
    • Defining the Acquisition Timing
    • Initial Operations
    • Enabling Pre-Processing Operations
  • Image Data Saving
    • File-based Saving
    • DICOM Saving
    • DICOM C-STORE
    • Database Saving
    • Buffer Saving
  • Component Data Loading and Saving
    • Loading/Saving without Database Option
    • Loading/Saving with Database Option
    • Loading of Vector Data
• Image Display and Basic Processing
  • Viewing and Changing Study Information
    • Modality Info
    • Image Properties
    • Subject, Study and SUV-related Information
    • Image History and Macros
    • Protocols
  • Changing the Image Presentation
  • Configuring the Layout
  • Image Zooming
  • Data Inspector
    • SUV Value Inspection and Statistics
  • Handy Image Processing Tools
  • Image Processing Tools
    • Average (Frames & Slices)
    • Automatic Brain VOIs (PFUS Option)
    • Background Removal
    • CT Table Removal
    • Defacing
    • Edge Enhancement
    • Endian Switching
    • Energy Masking
    • External Script
    • Filter
    • Gradient Vector Flow
    • Histogram
    • ImageJ
    • Interpolation
    • ITK Image Filters
    • Motion Correction (PFUS option)
    • Morphological
    • MRI DWI
    • MRI Probability / Inhomogeneity
    • MRI Signal to Concentration
    • MRI Skull Stripping (PFUS option)
    • MRI T1 Map
    • Noise Addition
    • Numeric Operations
    • Principal Component Analysis
    • PVC (VOI based)
    • PVC (Brain MR based)
    • R Console
    • Reduce Matrix
    • Registration and Normalization (PFUS Option)
    • Replace Values
    • Resize
    • Scale Values
    • Segmentation
      • Mapping of Pixels from Scatter Plots
      • Skeletonization
    • Standard Orientation
    • SUV Image Calculation
    • Temporal Resampling
    • Texture Analysis
    • Wavelet Filtering
    • z-Score in VOI
    • Macro
  • Reslicing of the Images at Oblique Orientations
  • Adding Iso-Contour Lines to Images
  • Showing and Saving Movies
  • Image Capture
  • Reports
  • Presentation of Fused Images
  • 3D Volume Rendering, Rotating MIP Images
  • Markers
  • Curve Display
• Volume-of-Interest (VOI) Analysis
  • VOI Interface
  • Using Contour VOIs
    • VOI and Contour Properties
      • VOI Level Properties
      • ROI and Contour Level Properties
      • Contour Display Properties
      • Inclusion Criteria for Pixels
      • Overlapping Control
      • Overlay Statistics
    • Contour Definition Tools
      • Preparations
      • Contouring Workflow
      • Neutral Mode
      • Undo/Redo
      • Outline Polygon
      • Adding/Removing individual Pixels
      • Draw Contour
      • Paint ROI
      • Regular VOIs
      • Interactive 3D Iso-contouring
      • Interactive 2D Iso-contouring
      • Controlled/Restricted Iso-contouring
      • Contour Interpolation
      • VOIs from Label Maps
    • Special-purpose Sub-VOIs
      • Hottest Pixels
      • Sphere at Max
      • Sphere with Max Average (Peak VOI)
      • Tumor Volume Segmentation
      • Hottest Connected Pixels
    • Hot-keys Based Lesion Segmentation
      • Peak VOI
      • Isocontour VOI
      • PERCIST-type Iso-contouring VOI based on Reference VOI
    • Adjustment Tools for Contour VOIs
      • Editing Contour Shapes
      • CTR Toolbar
      • ROI Toolbar
      • VOI Toolbar
      • Spatial Transformation of VOIs
      • Split VOI
      • Change Definition Plane
      • Erosion/Dilation
      • Remove Staircase Effect
      • Make DICOM RTSS compatible
      • Remove Invisible VOI
    • Mask-based VOI Tool: Raster VOIs
      • Outline Segments to Mask VOIs
      • Create/Edit Mask VOI
      • Raster VOIs Statistics
      • Save/Load of the Raster VOIs
    • VOI Sorting
    • VOI Grouping
    • VOI Save/Load
    • 3D VOI Visualization
  • Using VOI Atlas Files
    • Structure of VOI Atlases in PMOD
    • Tree Organization of Atlas VOIs
    • Atlas-based VOI Statistics
    • Converting Atlas VOIs to Contour VOIs using Outline
    • Converting Atlas VOIs to Contour VOIs using Normalize
    • Probabilistic VOI Atlas
    • VOI Atlases included in PMOD
      • Single-Subject AAL Human Brain Atlas
      • Amyloid Cortical Composite Atlas
      • Centiloid Atlas
      • Cynomolgus Monkey Atlas
      • Rhesus Macaque (INIA19)
      • Domestic Pig / Minipig Brain Atlas (CH.Malbert)
      • Sprague-Dawley Rat Brain Atlas (A.Schwarz) & PET/SPECT Templates (Groningen)
      • Sprague-Dawley Rat Brain Atlas (Schiffer)
      • Wistar Rat Brain Atlas (Tohoku)
      • Mouse Brain Atlas (Ma-Benveniste-Mirrione)
      • Preparation of VOI Atlas Files for PMOD
  • Using Label Map Files
  • Using Mask Files
  • Applying VOI Definitions
    • Statistics of VOI Pixel Values
      • Statistics Measures
      • Statistics Viewer
      • Histogram
      • Pixel Dump
      • File-Based Statistics
      • Texture Analysis
    • Data Modification
      • VOI-based Image Cropping
      • Data Masking Inside and Outside of VOIs
      • Algebra within VOIs
      • Interactive Data Masking
    • Time-Activity Curves
      • Time-Activity Curve Generation with Transfer to PKIN
      • Time-Activity Curve Generation with Statistics
    • Creation of a VOI Atlas
  • Statistics Aggregation
    • Data Selection
    • Information Selection
    • Aggregate Generation and Saving
    • Aggregate Export and R Transfer
    • Aggregate Inspection and Combination with External Data
• R Statistics in PMOD
  • R Installation and Configuration
    • Windows
    • MAC OS
    • Linux
  • Starting the R Console
  • R Console Organization
  • Data Loading
  • R Variable Structure
  • Table Layout
  • Plotting Layout
    • Box Plots
    • Data Plots
    • Density Plots
    • Histogram Plots
    • Ladder Plots
    • Polar Plots
    • Scatter Plots
  • Analysis Scripts for Aggregates
    • ANOVA for 3 or 4 Groups
    • Bartlett Test
    • Bland Altman Plot
    • Descriptive Statistics
    • Difference
    • Kruskal-Wallis Test
    • Linear Models: Statistical Analysis of Regional Imaging Data
      • Data Structure - Master Table
      • rm-ANOVA/MANOVA
        • Overview
        • rm_ANOVA/MANOVA PMOD-R Implementation
      • Linear Mixed Effect Models (LME)
        • Overview
        • LME PMOD-R Implementation
      • Discrimination Analysis
        • Overview
        • LDA PMOD-R Implementation
          • Identification of the LDA Function
          • Prediction
      • References
    • Test-Retest
    • t-Test
    • Variance Analysis
    • Pixel Dump
  • Image Layout
  • Command Layout
  • User Programming and Scripts
    • Package Manager
    • Accessing PMOD R Variables
• Partial-Volume Correction (PVC)
  • PVC based on Manual and Brain Template VOIs
    • Methodology Description
    • Implemented VOI-based PVC Variants
    • Common Requirements
    • Results of VOI-based PVC
      • VOI Based Uniform (GTM)
      • Region-Based Voxelwise (RBV)
    • PVC using Manual VOIs
    • PVC using Template VOIs based on Standard Masks
    • PVC using Template VOIs based on Individual Masks
    • PVC using Template VOIs based on Plain VOIs
    • Recommendations
  • PVC of Brain Images based on MRI Segmentation
    • Methodology Description
    • Requirements
    • Performing MRI-based PVC
    • Validation and Recommendations
  • PVC References
• Pipeline Processing
  • Starting Pipeline Definition
  • Pipeline Definition User Interface
  • Use of External Tools for Pipeline Processing
  • Pipeline-only Tools
    • Quality Control (QC)
    • Replace Images
    • Macro
    • VOI Statistics
    • Kinetic Modeling (PKIN Option)
  • Detailed Pipeline Example: Kinetic Modeling with SRTM, Brain VOIs in PET Space
    • Association of MR and PET Series
    • Automatic Brain VOIs
    • Registration and Normalization
    • Replace Images
    • Motion Correction
    • Kinetic Modeling
    • Pipeline Input Data
    • Testing the Pipeline
    • Running the Pipeline
  • Pipeline Example: Brain Uptake Statistics, MR Space
  • List of Pipelines
  • Call PMOD Pipeline Processing from Command Script
    • Folder Structure
    • Pipeline Definition
    • Script Definition
• PMOD Image Viewing and VOI Tool (PVIEW)
  • Top Menu Line
  • Load - Page 1 (Option)
  • Preprocessing - Page 2
    • Tools
      • Merge Series Tool
      • Merge Slices & Stitching
    • Batch Format Conversion
    • Batch Anonymization
  • Volume-of-Interest Analysis - Page 3
  • Statistics - Page 4
  • Compare - Page 5
  • Image Hybrid - Page 6
  • Creation of a DICOMDIR File
• PMOD Disclaimer
• PMOD Copyright Notice