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<div align="center"><b><u> Wiki Concept</u></b></div>
 
<div align="center"><b><u> Wiki Concept</u></b></div>
  
<P>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.  
+
<P>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.</P>  
 
Also, there is a document section where useful documents can uploaded or downloaded by anyone in the group.</P>  
 
<p>The purpose of this is to facilitate
 
<p>The purpose of this is to facilitate
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===General Lab Topics===
 
===General Lab Topics===
 +
----
 
*[[Research Group Contact Info]]
 
*[[Research Group Contact Info]]
 
*[[Conferences]]
 
*[[Conferences]]
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*[[Documents]]
 
*[[Documents]]
 
*[[Current Problems]]
 
*[[Current Problems]]
*[[Archive]] Obsolete stuff here.
+
*[[Suggested Improvements to BME]]
  
===Administration===
+
===Lab Administration===
 +
----
 
*[[Hardware Purchasing]]
 
*[[Hardware Purchasing]]
 
*[[Laboratory Equipment List]]
 
*[[Laboratory Equipment List]]
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===Scanco MicroCT and VMS Workstations===
 
===Scanco MicroCT and VMS Workstations===
 
----
 
----
 +
* [http://www.ucalgary.ca/microct/documents/x-ray_how_to Detailed OpenVMS and Scanco MicroCT Instructions]
 
* [[Project Management]]
 
* [[Project Management]]
* [[Scanco MicroCT]]
 
 
* [[OpenVMS]]
 
* [[OpenVMS]]
 
: Basic usage of OpenVMS systems.
 
: Basic usage of OpenVMS systems.
* [[Evaluation]]
+
* [[Scanco MicroCT Operation]]
* [[Print outs and visualization]]
+
* [[MicroCT Evaluation and Analysis]]
* [[Writing Scripts]]
+
* [[Writing IPL Scripts]]
* [[File Transfer]]
 
 
* [[Errors and Fixes]]
 
* [[Errors and Fixes]]
 
* [[Scanco Medical FAQ]]
 
* [[Scanco Medical FAQ]]
 +
* [[Uploading MRI to Scanco]]
 +
 +
===Dual-energy X-ray absorptiometry (DXA)===
 +
----
 +
* [[Scanning guidelines]]
 +
 +
===Network Access===
 +
----
 +
* [[VPN Setup]]
 +
 +
  
 
|bgcolor="#CCCCCC"|
 
|bgcolor="#CCCCCC"|
 
|valign="top"|
 
|valign="top"|
 
===Visualization===
 
----
 
*[[Using ParaView]]
 
  
 
===Registration and Segmentation===
 
===Registration and Segmentation===
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*[[Scanco Image Registration]]
 
*[[Scanco Image Registration]]
 
*[[SimilarityRegistration]]
 
*[[SimilarityRegistration]]
 +
*[[skiRegistration]]
 +
*[[MRI to HR-pQCT Registration with Scanco]]
  
 
===Finite Element Modelling===
 
===Finite Element Modelling===
 
----
 
----
 +
*[[FAIM Finite Element Solver]]
 +
: This is the lab finite element software.
 
*[[Tutorial on Generating AIMs for FE Analysis]]
 
*[[Tutorial on Generating AIMs for FE Analysis]]
 
: First steps for processing microCT data for FE analysis.
 
: First steps for processing microCT data for FE analysis.
*[[Tutorial on building an FE model with python and vtkski]]
 
: Read this if you want to build FE models from microCT data, particularly if you have unusual boundary conditions.
 
 
*[[Scanco Finite Element Modelling]]
 
*[[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.
 
: 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.
 +
 +
===Visualization===
 +
----
 +
*[[Using ParaView]]
  
 
===Statistics===
 
===Statistics===
 +
----
 
*[[JAGS Usage]]
 
*[[JAGS Usage]]
 
: Analysis of Bayesian models using Markov Chain Monte Carlo
 
: Analysis of Bayesian models using Markov Chain Monte Carlo
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This section covers generic computer-related topics not covered in other sections.
 
This section covers generic computer-related topics not covered in other sections.
 
*[[Unix command line basics]]
 
*[[Unix command line basics]]
*[[ssh|Setting up Key Authentication for SSH]]
+
*[[ssh|SSH tricks]]
 
*[[Lab Server Configuration]]
 
*[[Lab Server Configuration]]
 +
*[[Computer for STARS software]] STARS is CMG's fluid modelling software.
  
 
|bgcolor="#CCCCCC"|
 
|bgcolor="#CCCCCC"|
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====Lab Software Projects====
 
====Lab Software Projects====
*[[Bone lab libraries]]
+
*[[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.
: A library of reusable bits for the kinds of things we do in the lab.  Built on VTK and ITK and other toolkits.
 
**[[vtkski development]]
 
**[[vtkMy development]]
 
 
*[[Bone lab applications]] provides a list of lab custom software.
 
*[[Bone lab applications]] provides a list of lab custom software.
*[[Writing Python scripts that use vtkski]]
 
*[[ParaView Extensions]]
 
: How to compile and use the lab ParaView Extensions.
 
*[[faim development]]
 
: FAIM is our finite element solver.
 
 
*[[SAP development]]
 
*[[SAP development]]
 
: SAP is a tool for visualizing and manipulating AIMs.
 
: 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.
  
 
====Platforms====
 
====Platforms====
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*[[Development for Linux]]
 
*[[Development for Linux]]
 
*[[Development on Windows]]
 
*[[Development on Windows]]
*[[Development on VMS]]
+
*[[Development on OpenVMS]]
  
 
====Languages and Toolkits====
 
====Languages and Toolkits====
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*[[Creating VTK Classes]]
 
*[[Creating VTK Classes]]
 
*[[ITK Development]]
 
*[[ITK Development]]
 +
*[[Matlab Development]]
 +
*[[Writing plugins for ParaView]]
  
 
====Development Tools====
 
====Development Tools====
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----
 
----
 
*[[Wireless Network in Morphometrics Lab]]
 
*[[Wireless Network in Morphometrics Lab]]
 +
*[[Archive]] Obsolete stuff here.
  
 
|}
 
|}

Revision as of 07:36, 14 June 2017


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.

Smaller bone loss.jpg

Contents

General Lab Topics


Lab Administration


Scanco MicroCT and VMS Workstations


Basic usage of OpenVMS systems.

Dual-energy X-ray absorptiometry (DXA)


Network Access



Registration and Segmentation


Finite Element Modelling


This is the lab finite element software.
First steps for processing microCT data for FE analysis.
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.

Visualization


Statistics


Analysis of Bayesian models using Markov Chain Monte Carlo

Computers


This section covers generic computer-related topics not covered in other sections.

Developer


Lab Software Projects

SAP is a tool for visualizing and manipulating AIMs.
Image guided failure assessment device (aka the cannon) can be controlled from PC via serial port.

Platforms

Obtaining, compiling and installing software development tools on various systems.

Languages and Toolkits

Development Tools

Miscellaneous




A link back to: Steve Boyd's homepage

To return to the Lab home page: Biomedical Imaging Metrics Homepage