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Bone Imaging Laboratory Wiki

Wiki Concept The idea of the 'Wiki' site is that any authorized user, in this case a member of the lab, can see and edit any of the pages on this site, as well as create new pages as required. Also, there is a document section where useful documents can uploaded or downloaded by anyone in the group. The purpose of this is to facilitate information exchange within the lab and keep up-to-date How To and User Manuals for all lab procedures.

Contents

Scanco User Instructions OpenVMS Basics Beginner's Reference Session Manager DEC Terminal and DCL DCL Programming Guide List of basic commands Micro-CT Basics User Tutorials µCT Image Basics Image Data Scanco Medical µCT Software Scanning Sample Name Convention Register Samples for Scanning Log Sheets Patient Casts and Sample Holders Scan Parameters (Controlfiles) Perform a Scan Action on Image Artifacts Evaluation Evaluate a Scan Draw Contours Evaluation Scripts IPL Scripting Results Images and Animations Image Tours Extract Results Generate Report Data Management Trainee’s Data Responsibility Move data from Data Disk to Project Disk Import and Export Import Foreign Data Import MRI Images Import Xradia *.bin Get Your Files Remote Access VPN Setup Setup for MAC/Linux Setup for Windows Remote Access FAQ Books and References Imaging Essential Physics of Medical Imaging Bone Books on Bone Bone Morphometry and Densitometry		Scanco Administration OpenVMS OpenVMS References Unix related Graphical Applications File Operations Administrative Commands Calibration and QC System Updates Calibration and Conversion Quality Control (QC) Scanning Scanner User Manual Scanco's FAQ Scan Reconstruction Manipulate RSQ Manipulate ISQ Image Artifacts Evaluation Analysis Topics UCT_EVALUATION Evaluation FAQ IPL FAQ Results Extract Results Database Other FAQ Data Management Lab’s Data Responsibility HP Server and Disk Array Tape USB_Drive CDROM Saveset and Zip files Backup and Archive Process, Printer and System Processes and Jobs Printer System Remote Access For Scanco support Access VMS filesystem Setup other remote access Physical connections Dose Dose Calculations Optimize Scan for Low Dose		Xradia Instructions User Tutorials Scanning Reconstruction Special Topics Dual-Energy Imaging Phase Contrast Imaging Image Registration Scanco Image Registration Image Transformation Image Registration Register MRI to HR-pQCT SimilarityRegistration Understand rotation parameters Set optimizer scales skiRegistration ITK Rigid registration for HR-pQCT Finite Element Modelling Scanco Finite Element Modelling FAIM Finite Element Solver FE Tutorial Prepare AIMs for FE Analysis Developer Software Plugins and Codes ImageJ Plugin for AIM ISQ RSQ files Amira Script for AIM files Bone lab libraries A library of reusable bits for the kinds of things we do in the lab. Built on VTK and ITK and other toolkits. Bone lab applications provides a list of lab custom software. SAP development SAP is a tool for visualizing and manipulating AIMs. IGFA control Image guided failure assessment device (aka the cannon) can be controlled from PC via serial port. JAGS Statistics Analysis of Bayesian models using Markov Chain Monte Carlo ParaView Subversion (SVN) for accessing the source code of lab software. Platforms Obtaining, compiling and installing software development tools on various systems. Development on OS-X Development for Linux Development on Windows Development on OpenVMS Languages and Toolkits C++ Development Creating VTK Classes ITK Development Matlab Development Writing plugins for ParaView Miscellaneous Archive Obsolete stuff here. This section covers generic computer-related topics not covered in other sections. Unix command line basics SSH tricks Lab Server Configuration

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