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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 Bone Morphometry and Densitometry Suggested readings Model-Independent (Direct) Structural Measurements Densitometric Measurements Scanning Sample Name Convention Register Samples for Scanning Log Sheets Patient Casts and Sample Holders Scan Parameters (Controlfiles) Perform a Scan Image Artifacts Evaluation Evaluate a Scan Draw Contours Evaluation Scripts IPL Scripting Results Images and Animations Extract Results Generate Report Data Management Trainee’s Data Responsibility Move data from Data Disk to Project Disk Export and Import Get Your Files Import Foreign Data Import MRI Images Import Xradia *.bin Remote Access VPN Setup Setup for MAC/Linux Setup for Windows Remote Access FAQ		Scanco Administration OpenVMS OpenVMS References Unix related Graphical Applications File Operations Administrative Commands Calibration and QC System Updates Calibration and Conversion Beam Hardening Correction (BHC) Quality Control (QC) Scanning Scanner User Manual Scanco's FAQ Scanning FAQ Reconstruction Manipulate RSQ Manipulate ISQ Evaluation Analysis Topics UCT_EVALUATION Evaluation FAQ IPL FAQ Results Extract Results Database Other FAQ Data Management Lab’s Data Responsibility 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		Registration and Segmentation Scanco Image Registration SimilarityRegistration skiRegistration MRI to HR-pQCT Registration with Scanco Finite Element Modelling FAIM Finite Element Solver This is the lab finite element software. Tutorial on Generating AIMs for FE Analysis First steps for processing microCT data for FE analysis. Scanco Finite Element Modelling We typically use our own FE solver, faim. This documentation may however be useful if you want for example to make comparisons with Scanco's FE solver. 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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