- @ -

@ FTP Nodes

- 3 -

3D VOI Visualization

3D Volume Rendering, Rotating MIP Images

- A -

Access to Console Output

Accessing PMOD R Variables

Adding Iso-Contour Lines to Images

Adding/Removing individual Pixels

Administrative Tools

Aggregate Export and R Transfer

IconAggregate Export and R Transfer
IconData Loading

Aggregate Generation and Saving

Aggregate Inspection and Combination with External Data

Aggregation of Components such as VOIs and Kinetic Parameters

Analysis Scripts for Aggregates

ANOVA for 3 or 4 Groups

IconANOVA for 3 or 4 Groups
IconBartlett Test
IconKruskal-Wallis Test
IconVariance Analysis

Applying VOI Definitions

Association of MR and PET Series

Atlas-based VOI Statistics

Auto Iso-contour VOIs

IconControlled/Restricted Iso-contouring
IconSpecial-purpose Sub-VOIs

Automatic Brain VOIs

Automatic Brain VOIs (PFUS Option)

Average (Frames & Slices)

- B -

Background Removal

Bartlett Test

IconBartlett Test
IconVariance Analysis

Basic User Interface Elements

IconBasic User Interface Elements
IconData Selection

Bland Altman Plot

Box Plots

IconBox Plots
IconANOVA for 3 or 4 Groups
IconDescriptive Statistics
IconIdentification of the LDA Function

Buffer Loading

Buffer Saving

IconBuffer Loading
IconBuffer Saving

- C -

Changing the Image Orientation

IconFormat Descriptions
IconChanging the Image Orientation

Changing the Image Presentation

IconChanging the Image Presentation
IconSUV Value Inspection and Statistics

Combination of License and Database Server

IconCombination of License and Database Server
IconCombination of License and Database Server
IconCombination of License and Database Server

Command Layout

IconPlotting Layout
IconCommand Layout

Common Requirements

Component Data Loading

IconComponent Data Loading
IconLoading/Saving with Database Option

Component Data Loading and Saving

Component Data Saving

IconComponent Data Saving
IconLoading/Saving with Database Option

CONFIDENCE CONNECTED (ITK)

IconSegmentation
IconCONFIDENCE CONNECTED (ITK)

Configuration Backup/Restore

Configuring the Layout

CONNECTED THRESHOLD (ITK)

IconSegmentation
IconCONNECTED THRESHOLD (ITK)

Contour Definition Tools

Contour Display Properties

Contour Drawing Mode

Contour Interpolation

Converting Atlas VOIs to Contour VOIs using Normalize

Converting Atlas VOIs to Contour VOIs using Outline

Creation and Configuration of Databases

IconCreation and Configuration of Databases
IconExternal Backup Procedure

Creation of a DICOMDIR File

Creation of Atlas VOIs

CT Table Removal

CTR Toolbar

Curve Association

IconCurve Association
IconKinetic Modeling (PKIN Option)

Curve Display

Cynomolgus Monkey Atlas

- D -

Data Association

Data Inspector

Data Loading

IconR Console Organization
IconData Loading

Data Loading and Saving

Data Plots

Data Selection

Data Structure - Master Table

Data Units

Database Administration

Database Loading

Database Loading - Page 1 (Option)

Database Saving

Defining the Acquisition Timing

Density Plots

Descriptive Statistics

Detailed Pipeline Example: Kinetic Modeling with SRTM, Brain VOIs in PET Space

IconPipeline Processing
IconReplace Images
IconVOI Statistics
IconKinetic Modeling (PKIN Option)
IconDetailed Pipeline Example: Kinetic Modeling with SRTM, Brain VOIs in PET Space
IconPipeline Example: Brain Uptake Statistics, MR Space

DICOM Advanced Options

DICOM Client Configuration

IconDICOM Client Configuration
IconDICOM Query/Retrieve

DICOM Part 10 Data Loading

IconImage Data Loading
IconDICOM Loading
IconCreation of a DICOMDIR File

DICOM Part 10 Data, C-STORE

DICOM Query Loader (Auxiliary Server)

DICOM Query/Retrieve

IconDICOM Query/Retrieve
IconImage Data Loading
IconDICOM Loading

DICOM Server Configuration

IconDICOM Server Configuration
IconDICOM Query/Retrieve

DICOM Server Properties

DICOM Server Starting

DICOM Special Cases

Difference

Directory Tree

Discrimination Analysis

Domestic Pig / Minipig Brain Atlas (CH.Malbert)

- E -

Edge Enhancement

Editing Contour Shapes

Enabling Pre-Processing Operations

Endian Switching

Energy Masking

Environment and Prerequisites

Erosion/Dilation

Execution of PMOD Pipeline Processing from Script

Export and Backup of Database Contents

External Backup Procedure

External Script

External Tools

IconHandy Image Processing Tools
IconExternal Tools
IconTexture Analysis
IconImage Layout
IconPipeline Processing
IconUse of External Tools for Pipeline Processing

- F -

File-based loading

File-based Saving

File-Based Statistics

Filter

IconHandy Image Processing Tools
IconFilter

Folders Structure

Format Descriptions

Format Overview

- G -

General Configuration

IconGeneral Configuration
IconPMOD Server Administration
IconInclusion Criteria for Pixels
IconPMOD Network Clients Installation and Configuration
IconPMOD Network Clients Installation and Configuration
IconPMOD Network Clients Installation and Configuration

GM & WM & CSF Probability (PFUS option)

IconData Association
IconGM & WM & CSF Probability (PFUS option)

Gradient Vector Flow

- H -

Handy Image Processing Tools

Histogram

IconHistogram
IconHistogram

Histogram Plots

Hot-keys Based Lesion Segmentation

Hottest Connected Pixels

Hottest Pixels

HOTTEST PIXELS Segmentation

IconSegmentation
IconHOTTEST PIXELS Segmentation

- I -

Identification of the LDA Function

Image Association

IconImage Association
IconReplace Images
IconDetailed Pipeline Example: Kinetic Modeling with SRTM, Brain VOIs in PET Space
IconPipeline Example: Brain Uptake Statistics, MR Space

Image Capture

Image Comparison - Page 4

Image Data Formats

Image Data Loading

IconImage Data Loading
IconDatabase Administration
IconImage Data Loading
IconDatabase Loading
IconDatabase Loading - Page 1 (Option)
IconImage Viewing - Page 2

Image Data Saving

IconImage Data Saving
IconImage Data Saving
IconDatabase Saving

Image Data Transformations during Loading

IconImage Data Transformations during Loading
IconPipeline Definition User Interface

Image Display and Basic Processing

IconImage Display and Basic Processing
IconImage Viewing - Page 2

Image Fusion - Page 5 (Optional)

Image History and Macros

IconLoading Macros
IconImage History and Macros
IconMacro
IconMacro

Image Layout

Image Properties

IconImage Properties
IconConfiguring the Layout

Image Viewing - Page 2

Image Zooming

ImageJ

Implementation of DICOM Servers on a Dedicated Machine

Implemented VOI-based PVC Variants

IN RANGE Segmentation

IconSegmentation
IconIN RANGE Segmentation

Inclusion Criteria for Pixels

IconInclusion Criteria for Pixels
IconStatistics Measures

Incoming Folder

Information Selection

IconInformation Selection
IconData Structure - Master Table

Initial Operations

Inspecting Associations

Installation Overview

Interpolation

IconInterpolation
IconReduce Matrix

Iso-contour Mode (Pseudo-Snake)

ITK Image Filters

- K -

Keyboard Shortcuts

IconBasic User Interface Elements
IconKeyboard Shortcuts

Kinetic Modeling

Kinetic Modeling (PKIN Option)

IconPipeline-only Tools
IconKinetic Modeling (PKIN Option)

Kruskal-Wallis Test

IconKruskal-Wallis Test
IconVariance Analysis

- L -

Ladder Plots

IconLadder Plots
IconDescriptive Statistics

LDA PMOD-R Implementation

Linear Mixed Effect Models (LME)

Linear Models: Statistical Analysis of Regional Imaging Data

Linux Installation

List of Pipelines

IconPipeline Processing
IconList of Pipelines

LME PMOD-R Implementation

Loading Data from Databases

Loading Macros

IconLoading Macros
IconImage History and Macros

Loading of Vector Data

Loading/Saving with Database Option

Loading/Saving without Database Option

- M -

Mac OS X Installation

Macro

IconMacro
IconMacro

Management using AlwaysUp Web Service

Mapping of Pixels from Scatter Plots

IconSegmentation
IconMapping of Pixels from Scatter Plots

Markers

Masking Inside and Outside of VOIs

Merge Frames Tool

IconImage Viewing - Page 2
IconMerge Frames Tool

Merge Slices & Stitching

Methodology Description

IconMethodology Description
IconMethodology Description

Modality Info

MODULES

Morphological

IconMorphological
IconErosion/Dilation

Motion Correction

Motion Correction (PFUS option)

Mouse Brain Atlas (Ma-Benveniste-Mirrione)

MRI DWI

MRI Probability / Inhomogeneity

MRI Signal to Concentration

MRI Skull Stripping (PFUS option)

MRI T1 Map

IconMRI Signal to Concentration
IconMRI T1 Map

Multiple DICOM Server Creation

- N -

NEIGHBORHOOD CONNECTED (ITK)

IconSegmentation
IconNEIGHBORHOOD CONNECTED (ITK)

No Saw

Noise Addition

Numeric Operations

- O -

On Start

IconOn Start
IconProblem Reporting
IconHot-keys Based Lesion Segmentation

OTSU THRESHOLD (ITK)

IconSegmentation
IconOTSU THRESHOLD (ITK)

Outline Object Label Maps

Outline Segments

Overlapping Control

Overview

IconOverview
IconOverview
IconOverview

- P -

Package Use

Paint ROI by Circle (2D)

Partial-Volume Correction (PVC)

IconExternal Tools
IconPVC (VOI based)
IconPVC (Brain MR based)
IconPartial-Volume Correction (PVC)

Patient, Study and SUV-related Information

Peak VOI and Iso-contouring VOI

IconData Inspector
IconPeak VOI

PERCIST-type Iso-contouring VOI based on Liver VOI

Performing MRI-based PVC

PET Tumor Volume Segmentation

Pipeline Definition

Pipeline Definition User Interface

Pipeline Example: Brain Uptake Statistics, MR Space

Pipeline Input Data

Pipeline Processing

IconWhat happens with received DICOM Images
IconData Association
IconExternal Tools
IconMacro
IconPipeline Processing

Pipeline-only Tools

Pixel Dump

IconPixel Dump
IconData Loading
IconPixel Dump

Plotting Layout

PMOD Base Functionality Introduction

PMOD Basics

PMOD Copyright Notice

PMOD Database Functionality

IconGeneral Configuration
IconPMOD Database Functionality
IconPMOD Server Administration
IconPipeline Processing

PMOD DICOM Functionality

IconGeneral Configuration
IconPMOD DICOM Functionality
IconPMOD Server Administration
IconCreation of a DICOMDIR File

PMOD Image Viewing and VOI Tool (PVIEW)

PMOD Installation and Maintenance

PMOD License Server Installation

IconPMOD Server Administration
IconPMOD License Server Installation
IconPMOD License Server Installation
IconPMOD License Server Installation

PMOD Network Clients Installation and Configuration

IconPMOD Network Clients Installation and Configuration
IconPMOD Network Clients Installation and Configuration
IconPMOD Network Clients Installation and Configuration

PMOD Network License Installation

IconPMOD Stand-alone License Installation
IconPMOD Network License Installation
IconPMOD Network License Installation
IconPMOD Network License Installation

PMOD Server Administration

IconDICOM Server Starting
IconSetting up a Transaction Server to Publish a Database
IconPMOD Server Administration

PMOD Server Processes as Windows Services

IconImplementation of DICOM Servers on a Dedicated Machine
IconSetting up a Transaction Server to Publish a Database
IconPMOD Server Processes as Windows Services

PMOD Software Extraction

IconPMOD Software Extraction
IconPMOD Software Extraction
IconPMOD Software Extraction

PMOD Stand-alone License Installation

IconPMOD Stand-alone License Installation
IconPMOD License Server Installation
IconPMOD Network Clients Installation and Configuration
IconPMOD Stand-alone License Installation
IconPMOD License Server Installation
IconPMOD Network Clients Installation and Configuration
IconPMOD Stand-alone License Installation
IconPMOD License Server Installation
IconPMOD Network Clients Installation and Configuration

PMOD ToolBox

IconPMOD DICOM Functionality
IconCreation and Configuration of Databases
IconPMOD ToolBox

Polar Plots

Prediction

Preparation of VOI Atlas Files for PMOD

Preparations

Presentation of Fused Images

IconPresentation of Fused Images
IconImage Comparison - Page 4

Principal Component Analysis

Probabilistic VOI Atlas

IconProbabilistic VOI Atlas
IconStatistics Measures

Problem Reporting

IconProblem Reporting
IconImage Capture
IconR Console Organization

PVC (Brain MR based)

IconData Association
IconPVC (Brain MR based)

PVC (VOI based)

PVC based on Manual and Brain Template VOIs

PVC of Brain Images based on MRI Segmentation

PVC References

PVC using Manual VOIs

PVC using Template VOIs based on Individual Masks

PVC using Template VOIs based on Plain VOIs

PVC using Template VOIs based on Standard Masks

PXMOD, PKIN, READ/WRITE, LOADING, Color Tables Plug-ins

- Q -

Quality Control (QC)

IconPipeline Definition User Interface
IconPipeline-only Tools
IconQuality Control (QC)

- R -

R Console

R Console Organization

IconStatistics Viewer
IconR Console Organization

R Installation and Configuration

IconSETTINGS
IconR Installation and Configuration

R Statistics in PMOD

IconSETTINGS
IconStatistics Viewer
IconR Statistics in PMOD

R Variable Structure

IconR Variable Structure
IconPlotting Layout
IconAccessing PMOD R Variables

Recommendations

Reduce Matrix

IconHandy Image Processing Tools
IconReduce Matrix

References

REGION GROWING Segmentation

IconSegmentation
IconREGION GROWING Segmentation

Region-Based Voxelwise (RBV)

Registration and Normalization

Registration and Normalization (PFUS Option)

Regular VOIs

Replace Images

IconPipeline-only Tools
IconReplace Images
IconReplace Images

Replace Values

IconHandy Image Processing Tools
IconReplace Values

Replication from one Database to Another

Reports

Requirements

Resize

Reslicing of the Images at Oblique Orientations

Results of VOI-based PVC

rm_ANOVA/MANOVA PMOD-R Implementation

rm-ANOVA/MANOVA

ROI and Contour Level Properties

IconVOI Level Properties
IconROI and Contour Level Properties
IconVOI Grouping

ROI Toolbar

Running the Pipeline

- S -

Saving Data to Databases

Scale Values

IconHandy Image Processing Tools
IconScale Values

Scatter Plots

Script Definition

Segmentation

IconSegmentation
IconPartial-Volume Correction (PVC)

Server Administration Interface

Server Starting/Stopping

Services Administration

Setting up a Transaction Server to Publish a Database

IconImplementation of DICOM Servers on a Dedicated Machine
IconCreation and Configuration of Databases
IconSetting up a Transaction Server to Publish a Database
IconPMOD Server Administration
IconCombination of License and Database Server
IconCombination of License and Database Server
IconCombination of License and Database Server

SETTINGS

IconSETTINGS
IconStatistics Measures
IconData Loading

Showing and Saving Movies

IconShowing and Saving Movies
Icon3D Volume Rendering, Rotating MIP Images

Single-Subject AAL Human Brain Atlas

Skeletonization

Special-purpose Sub-VOIs

Sphere at Max

Sphere with Max Average (Peak VOI)

Sprague-Dawley Rat Brain Atlas (A.Schwarz) & PET/SPECT Templates (Groningen)

Sprague-Dawley Rat Brain Atlas (Schiffer)

Standard Orientation

Starting

Starting Pipeline Definition

IconStarting Pipeline Definition
IconAutomatic Brain VOIs

Starting the R Console

Statistics

IconSUV Value Inspection and Statistics
IconStatistics of VOI Pixel Values

Statistics Aggregation

IconStatistics Aggregation
IconR Console Organization
IconData Loading
IconAnalysis Scripts for Aggregates

Statistics Measures

IconInclusion Criteria for Pixels
IconProbabilistic VOI Atlas
IconStatistics Measures
IconVOI Statistics

Statistics Viewer

IconSUV Image Calculation
IconStatistics Viewer
IconData Loading

Structure of VOI Atlases in PMOD

Supported Platforms

SUV Image Calculation

IconSUV Value Inspection and Statistics
IconSUV Image Calculation

SUV Value Inspection and Statistics

IconSETTINGS
IconDICOM Saving
IconSubject, Study and SUV-related Information
IconChanging the Image Presentation
IconSUV Value Inspection and Statistics
IconStatistics Viewer

- T -

Table Layout

Testing the Pipeline

Test-Retest

Texture Analysis

IconTexture Analysis
IconTexture Analysis

THRESHOLD Segmentation

IconSegmentation
IconTHRESHOLD Segmentation

Time-Activity Curve Generation with Statistics

Time-Activity Curve Generation with Transfer to PKIN

Tool Configurations

IconTool Configurations
IconVOI Interface

Transform VOI to RT compatible

Tree Organization of Atlas VOIs

IconTree Organization of Atlas VOIs
IconDomestic Pig / Minipig Brain Atlas (CH.Malbert)
IconSprague-Dawley Rat Brain Atlas (A.Schwarz) & PET/SPECT Templates (Groningen)

Troubleshooting

IconTroubleshooting
IconTroubleshooting
IconTroubleshooting

t-Test

- U -

Undo/Redo/Neutral

Use of External Tools for Pipeline Processing

User Creation

User Programming and Scripts

USERS

User-Specific Database Preferences

IconSETTINGS
IconUser-Specific Database Preferences

Using Contour VOIs

Using Label Maps Files

IconVOIs from Label Maps
IconUsing Label Map Files

Using Mask Files

Using VOI Atlas Files

IconUsing VOI Atlas Files
IconUsing Label Map Files
IconUsing Mask Files

- V -

Validation and Recommendations

Variance Analysis

Version Upgrade in a Complex PMOD Environment

Vertex Edit Mode

Viewing and Changing Study Information

VOI Adjustment Tools

VOI Association

VOI Atlases included in PMOD

VOI Based Partial-Volume Correction (GTM Method)

IconMethodology Description
IconVOI Based Partial-Volume Correction (GTM Method)

VOI Based Uniform (GTM)

VOI Grouping

VOI Interface

VOI Level Properties

VOI Save/Load

VOI Statistics

VOI Toolbar

VOI-based Image Cropping

Volume-of-Interest (VOI) Analysis

IconVolume-of-Interest (VOI) Analysis
IconVolume-of-Interest Analysis - Page 3

Volume-of-Interest Analysis - Page 3

- W -

Wavelet Filtering

What happens with received DICOM Images

IconWhat happens with received DICOM Images
IconPipeline Processing

Windows Installation

Wistar Rat Brain Atlas (Tohoku)

- Z -

z-Score in VOI