- 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

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

Applying VOI Definitions

Association of MR and PET Series

Atlas-based VOI Statistics

Auto Iso-contour VOIs

Automatic Brain VOIs

Automatic Brain VOIs (PFUS Option)

Average (Frames & Slices)

- B -

Background Removal

Bartlett Test

Basic User Interface Elements

Bland Altman Plot

Box Plots

Buffer Loading

Buffer Saving

- C -

Changing the Image Orientation

Changing the Image Presentation

Combination of License and Database Server

Command Layout

Common Requirements

Component Data Loading

Component Data Loading and Saving

Component Data Saving

CONFIDENCE CONNECTED (ITK)

Configuration Backup/Restore

Configuring the Layout

CONNECTED 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

Creation of a DICOMDIR File

Creation of Atlas VOIs

CT Table Removal

CTR Toolbar

Curve Association

Curve Display

Cynomolgus Monkey Atlas

- D -

Data Association

Data Inspector

Data 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

DICOM Advanced Options

DICOM Client Configuration

DICOM Part 10 Data Loading

DICOM Part 10 Data, C-STORE

DICOM Query Loader (Auxiliary Server)

DICOM Query/Retrieve

DICOM Server Configuration

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

- F -

File-based loading

File-based Saving

File-Based Statistics

Filter

Folders Structure

Format Descriptions

Format Overview

- G -

General Configuration

GM & WM & CSF Probability (PFUS option)

Gradient Vector Flow

- H -

Handy Image Processing Tools

Histogram

Histogram Plots

Hot-keys Based Lesion Segmentation

Hottest Connected Pixels

Hottest Pixels

HOTTEST PIXELS Segmentation

- I -

Identification of the LDA Function

Image Association

Image Capture

Image Comparison - Page 4

Image Data Formats

Image Data Loading

Image Data Saving

Image Data Transformations during Loading

Image Display and Basic Processing

Image Fusion - Page 5 (Optional)

Image History and Macros

Image Layout

Image Properties

Image Viewing - Page 2

Image Zooming

ImageJ

Implementation of DICOM Servers on a Dedicated Machine

Implemented VOI-based PVC Variants

IN RANGE Segmentation

Inclusion Criteria for Pixels

Incoming Folder

Information Selection

Initial Operations

Inspecting Associations

Installation Overview

Interpolation

Iso-contour Mode (Pseudo-Snake)

ITK Image Filters

- K -

Keyboard Shortcuts

Kinetic Modeling

Kinetic Modeling (PKIN Option)

Kruskal-Wallis Test

- L -

Ladder Plots

LDA PMOD-R Implementation

Linear Mixed Effect Models (LME)

Linear Models: Statistical Analysis of Regional Imaging Data

Linux Installation

List of Pipelines

LME PMOD-R Implementation

Loading Data from Databases

Loading Macros

Loading of Vector Data

Loading/Saving with Database Option

Loading/Saving without Database Option

- M -

Mac OS X Installation

Macro

Management using AlwaysUp Web Service

Mapping of Pixels from Scatter Plots

Markers

Masking Inside and Outside of VOIs

Merge Frames Tool

Merge Slices & Stitching

Methodology Description

Modality Info

MODULES

Morphological

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

Multiple DICOM Server Creation

- N -

NEIGHBORHOOD CONNECTED (ITK)

No Saw

Noise Addition

Numeric Operations

- O -

On Start

OTSU THRESHOLD (ITK)

Outline Object Label Maps

Outline Segments

Overlapping Control

Overview

- P -

Package Use

Paint ROI by Circle (2D)

Partial-Volume Correction (PVC)

Patient, Study and SUV-related Information

Peak VOI and Iso-contouring 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

Pipeline-only Tools

Pixel Dump

Plotting Layout

PMOD Base Functionality Introduction

PMOD Basics

PMOD Copyright Notice

PMOD Database Functionality

PMOD DICOM Functionality

PMOD Image Viewing and VOI Tool (PVIEW)

PMOD License Server Installation

PMOD Network Clients Installation and Configuration

PMOD Network License Installation

PMOD Server Administration

PMOD Server Processes as Windows Services

PMOD Software Extraction

PMOD Stand-alone License Installation

PMOD ToolBox

Polar Plots

Prediction

Preparation of VOI Atlas Files for PMOD

Preparations

Presentation of Fused Images

Principal Component Analysis

Probabilistic VOI Atlas

Problem Reporting

PVC (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)

- R -

R Console

R Console Organization

R Installation and Configuration

R Statistics in PMOD

R Variable Structure

Recommendations

Reduce Matrix

References

REGION GROWING Segmentation

Region-Based Voxelwise (RBV)

Registration and Normalization

Registration and Normalization (PFUS Option)

Regular VOIs

Replace Images

Replace 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

ROI Toolbar

Running the Pipeline

- S -

Saving Data to Databases

Scale Values

Scatter Plots

Script Definition

Segmentation

Server Administration Interface

Server Starting/Stopping

Services Administration

Setting up a Transaction Server to Publish a Database

SETTINGS

Showing and Saving Movies

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

Starting the R Console

Statistics

Statistics Aggregation

Statistics Measures

Statistics Viewer

Structure of VOI Atlases in PMOD

Supported Platforms

SUV Image Calculation

SUV Value Inspection and Statistics

- T -

Table Layout

Testing the Pipeline

Test-Retest

Texture Analysis

THRESHOLD Segmentation

Time-Activity Curve Generation with Statistics

Time-Activity Curve Generation with Transfer to PKIN

Tool Configurations

Transform VOI to RT compatible

Tree Organization of Atlas VOIs

Troubleshooting

t-Test

- U -

Undo/Redo/Neutral

Use of External Tools for Pipeline Processing

User Creation

User Programming and Scripts

USERS

User-Specific Database Preferences

Using Contour VOIs

Using Label Maps Files

Using Mask Files

Using VOI Atlas 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)

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

Volume-of-Interest Analysis - Page 3

- W -

Wavelet Filtering

What happens with received DICOM Images

Windows Installation

Wistar Rat Brain Atlas (Tohoku)

- Z -

z-Score in VOI