PMOD Base Functionality Introduction
PMOD Basics
Basic User Interface Elements
Directory Tree
Starting
General Configuration
USERS
User Creation
SETTINGS
PXMOD, PKIN, READ/WRITE, LOADING, Color Tables Plug-ins
MODULES
@ FTP Nodes
On Start
PRESETS
Tool Configurations
Keyboard Shortcuts
Problem Reporting
PMOD DICOM Functionality
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)
PMOD Database Functionality
Creation and Configuration of Databases
Setting up a Transaction Server to Publish a Database
User-Specific Database Preferences
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
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
PMOD Server Administration
Data Loading and Saving
Image Data Formats
Format Overview
Format Descriptions
Image Data Loading
Data Units
DICOM Loading
File-based loading
Database 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
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
Edge Enhancement
Endian Switching
Energy Masking
External Script
Filter
Gradient Vector Flow
Histogram
ImageJ
Interpolation
ITK Image Filters
Macro
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
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
Outline Segments
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
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
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 Use
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)
Database Loading - Page 1 (Option)
Image Viewing - Page 2
Tools
Merge Frames Tool
Merge Slices & Stitching
Batch Format Conversion
Batch Anonymization
Volume-of-Interest Analysis - Page 3
Image Comparison - Page 4
Image Fusion - Page 5
Creation of a DICOMDIR File
PMOD Installation and Maintenance
Supported Platforms
Windows Installation
Installation Overview
PMOD Software Extraction
PMOD Stand-alone License Installation
PMOD Network License Installation
PMOD License Server Installation
PMOD Network Clients Installation and Configuration
Combination of License and Database Server
Version Upgrade in a Complex PMOD Environment
Troubleshooting
PMOD Server Processes as Windows Services
Environment and Prerequisites
Services Administration
Configuration Backup/Restore
Server Starting/Stopping
Access to Console Output
Management using AlwaysUp Web Service
Mac OS X Installation
Installation Overview
PMOD Software Extraction
PMOD Stand-alone License Installation
PMOD Network License Installation
PMOD License Server Installation
PMOD Network Clients Installation and Configuration
Combination of License and Database Server
Version Upgrade in a Complex PMOD Environment
Troubleshooting
Linux Installation
Installation Overview
PMOD Software Extraction
PMOD Stand-alone License Installation
PMOD Network License Installation
PMOD License Server Installation
PMOD Network Clients Installation and Configuration
Combination of License and Database Server
Version Upgrade in a Complex PMOD Environment
Troubleshooting
Server Administration Interface
PMOD Disclaimer
PMOD Copyright Notice