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__NOTOC__
 
__NOTOC__
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<center><b><font size="+3">Bone Imaging Laboratory Wiki</font></b>
 
<center><b><font size="+3">Bone Imaging Laboratory Wiki</font></b>
  
  
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+
<table width="100%" border="0">
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<table width="97%" border="0">
 
 
<tr>  
 
<tr>  
−
<td width="450" align="left" valign="middle" bgcolor="#ccff66">
+
<td width="15%" align="center" valign="middle" bgcolor="#ccff66">
 
<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, as well as create new pages as required.  
+
<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. </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
+
<br>
−
information exchange within the lab and keep up-to-date How To and User Manuals for all lab procedures.</P>
+
 
 +
<div align="center"><b><u> The Purpose</u></b></div>
 +
 
 +
<p>It's to facilitate information exchange within the lab and keep up-to-date How To and User Manuals for lab's technical procedures and FAQ.</P>
 +
 
 +
</td>
 +
 
 +
<td bgcolor="#ccff66">      [[File:BonelabScanners.JPG|center|750px]]</td>
 +
 
 +
<td width="25%" align="left" valign="middle" bgcolor="#ccff66">
 +
<div align="center"><b><u> Read me</u></b></div>
 +
 
 +
<p>
 +
#Use '''Ctr+F''' to search within any page.
 +
#Never include login credentials especially password anywhere.
 +
#It's all users' responsibility to keep the info precise, updated, abundant, and useful, through editing/addition/deletion as needed by clicking [edit] on the top-right corner of a page or item. This includes combining same/similar topics besides an item whenever appropriate.
 +
#Add a redirect line after each new item for consistency:
 +
#:[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]
 +
#Click '''Help''' on navigation list on the left penal for detailed editing instructions.
 +
#Contact Ying if you are not sure where to put a new item or could not find an item.
 +
</P>
 
</td>
 
</td>
  
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<td bgcolor="#ccff05">[[Image:Smaller_bone_loss.jpg]]</td>
 
 
</tr>
 
</tr>
 
</table>
 
</table>
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</center>
 
</center>
  
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== Contents ==
 
 
{| border="0" align="center" width="98%" valign="top" cellspacing="7" cellpadding="2"
 
{| border="0" align="center" width="98%" valign="top" cellspacing="7" cellpadding="2"
 
|-
 
|-
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|valign="top"|
 
|valign="top"|
  
−
===General Lab Topics===
+
==[[Scanco User Instructions]]==
−
----
+
[[Scanco_User_Instructions#OpenVMS_Basics| '''OpenVMS Basics''']]
−
*[[Research Group Contact Info]]
+
*[[Scanco_User_Instructions#OpenVMS_Beginner.27s_Reference| Beginner's Reference]]
−
*[[Conferences]]
+
*[[Scanco_User_Instructions#Session_Manager| Session Manager]]
−
*[[Journal Club]]
+
*[[Scanco_User_Instructions#DEC_Terminal_and_Digital_Command_Language_.28DCL.29| DEC Terminal and DCL]]
−
*[[Subject Recruitment]]
+
*[[Scanco_User_Instructions#DCL_Programming_Guide| DCL Programming Guide]]
−
*[[Publications]]
+
*[[Scanco_User_Instructions#List_of_basic_commands| List of basic commands]]
−
*[[Documents]]
+
 
−
*[[Current Problems]]
+
[[Scanco_User_Instructions#Micro-Computed_Tomography_.28.C2.B5CT.29_Basics| '''Micro-CT Basics''']]
 +
*[[Scanco_User_Instructions#User_Tutorials| User Tutorials]]
 +
*[[Scanco_User_Instructions#Micro-CT_Image_Basics| µCT Image Basics]]
 +
*[[Scanco_User_Instructions#Image_Data| Image Data]]
 +
*[[Scanco_User_Instructions#Scanco_Medical_Micro-CT_Software| Scanco Medical µCT Software]]
 +
 
 +
[[Scanco_User_Instructions#Scanning| '''Scanning''']]
 +
*[[Scanco_User_Instructions#Sample_Name_Convention| Sample Name Convention]]
 +
*[[Scanco_User_Instructions#Register_Samples_for_Scanning| Register Samples for Scanning]]
 +
*[[Scanco_User_Instructions#Log_Sheets| Log Sheets]]
 +
*[[Scanco_User_Instructions#Patient_Casts_and_Sample_Holders| Patient Casts and Sample Holders]]
 +
*[[Scanco_User_Instructions#Scan_Parameters_.28Controlfiles.29| Scan Parameters (Controlfiles)]]
 +
*[[Scanco_User_Instructions#Perform_a_Scan| Perform a Scan]]
 +
*[[Scanco_User_Instructions#Action_on_Image_Artifacts| Action on Image Artifacts]]
 +
 
 +
[[Scanco_User_Instructions#Evaluation| '''Evaluation''']]
 +
*[[Scanco_User_Instructions#Evaluate_a_Scan| Evaluate a Scan]]
 +
*[[Scanco_User_Instructions#Draw_Contours| Draw Contours]]
 +
*[[Scanco_User_Instructions#Evaluation_Scripts| Evaluation Scripts]]
 +
*[[Scanco_User_Instructions#Image_Processing_Language_.28IPL.29_Scripting| IPL Scripting]]
 +
 
 +
[[Scanco_User_Instructions#Results| '''Results''']]
 +
*[[Scanco_User_Instructions#Images_and_Animations| Images and Animations]]
 +
*[[Scanco_User_Instructions#Image_Tours| Image Tours]]
 +
*[[Scanco_User_Instructions#Extract_Results| Extract Results]]
 +
*[[Scanco_User_Instructions#Generate_Report| Generate Report]]
 +
 
 +
[[Scanco_User_Instructions#Data_Management| '''Data Management''']]
 +
*[[Scanco_User_Instructions#Trainee.E2.80.99s_Data_Responsibility| Trainee’s Data Responsibility]]
 +
*[[Scanco_User_Instructions#Move_data_from_Data_Disk_to_Project_Disk| Move data from Data Disk to Project Disk]]
  
−
===Lab Administration===
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[[Scanco_User_Instructions#Import_and_Export| '''Import and Export''']]
−
----
+
*[[Scanco_User_Instructions#Import_Foreign_Data_to_Scanco_System| Import Foreign Data]]
−
*[[Hardware Purchasing]]
+
*[[Scanco_User_Instructions#Import_MRI_to_Scanco_System| Import MRI Images]]
−
*[[Laboratory Equipment List]]
+
*[[Scanco_User_Instructions#Import_Xradia_.2A.bin_to_Scanco_System|Import Xradia *.bin]]
 +
*[[Scanco_User_Instructions#Get_Your_Files| Get Your Files]]
  
−
===Scanco MicroCT and VMS Workstations===
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[[Scanco_User_Instructions#Remote_Access| '''Remote Access''']]
−
----
+
*[[Scanco_User_Instructions#VPN_Setup| VPN Setup]]
−
* [[Project Management]]
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*[[Scanco_User_Instructions#Setup_for_MAC.2FLinux| Setup for MAC/Linux]]
−
* [[OpenVMS]]
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*[[Scanco_User_Instructions#Setup_for_Windows| Setup for Windows]]
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: Basic usage of OpenVMS systems.
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*[[Scanco_User_Instructions#Remote_Access_FAQ| Remote Access FAQ]]
−
* [[Scanco MicroCT Operation]]
 
−
* [[MicroCT Evaluation and Analysis]]
 
−
* [[Writing IPL Scripts]]
 
−
* [[Errors and Fixes]]
 
−
* [[Scanco Medical FAQ]]
 
  
 
|bgcolor="#CCCCCC"|
 
|bgcolor="#CCCCCC"|
 
|valign="top"|
 
|valign="top"|
  
−
===Visualization===
+
==[[Scanco Administration]]==
−
----
+
[[Scanco_Administration#OpenVMS| '''OpenVMS''']]
−
*[[Using ParaView]]
+
*[[Scanco_Administration#OpenVMS_References| OpenVMS References]]
 +
*[[Scanco_Administration#Unix_related| Unix related]]
 +
*[[Scanco_Administration#Graphical_Applications| Graphical Applications]]
 +
*[[Scanco_Administration#File_Operations| File Operations]]
 +
*[[Scanco_Administration#Administrative_Commands| Administrative Commands]]
 +
 
 +
[[Scanco_Administration#Calibration_and_QC | '''Calibration and QC''']]
 +
*[[Scanco_Administration#System_Updates| System Updates]]
 +
*[[Scanco_Administration#Calibration_and_Conversion| Calibration and Conversion]]
 +
*[[Scanco_Administration#Quality_Control_.28QC.29| Quality Control (QC)]]
 +
 
 +
[[Scanco_Administration#Scanning| '''Scanning''']]
 +
*[[Scanco_Administration#Scanner_User_Manual| Scanner User Manual]]
 +
*[[Scanco_Administration#Scanco.27s_FAQ| Scanco's FAQ]]
 +
*[[Scanco_Administration#Scan| Scan]]
 +
*[[Scanco_Administration#Reconstruction| Reconstruction]]
 +
*[[Scanco_Administration#Manipulate_RSQ| Manipulate RSQ]]
 +
*[[Scanco_Administration#Manipulate_ISQ| Manipulate ISQ]]
 +
*[[Scanco_Administration#Image_Artifacts| Image Artifacts]]
 +
 
 +
[[Scanco_Administration#Evaluation| '''Evaluation''']]
 +
*[[Scanco_Administration#Analysis_Topics| Analysis Topics]]
 +
*[[Scanco_Administration#UCT_EVALUATION| UCT_EVALUATION]]
 +
*[[Scanco_Administration#Evaluation_FAQ| Evaluation FAQ]]
 +
*[[Scanco_Administration#IPL_FAQ| IPL FAQ]]
 +
 
 +
[[Scanco_Administration#Results| '''Results''']]
 +
*[[Scanco_Administration#Extract_Results| Extract Results]]
 +
*[[Scanco_Administration#Database| Database]]
 +
*[[Scanco_Administration#Other_FAQ| Other FAQ]]
  
−
===Registration and Segmentation===
+
[[Scanco_Administration#Data_Management | '''Data Management''']]
−
----
+
*[[Scanco_Administration#Lab.E2.80.99s_Data_Responsibility| Lab’s Data Responsibility]]
−
*[[Scanco Image Registration]]
+
*[[Scanco_Administration#HP_Server_and_Disk_Array| HP Server and Disk Array]]
−
*[[SimilarityRegistration]]
+
*[[Scanco_Administration#Tape| Tape]]
 +
*[[Scanco_Administration#USB_Drive| USB_Drive]]
 +
*[[Scanco_Administration#CDROM| CDROM]]
 +
*[[Scanco_Administration#Saveset_and_Zip_files| Saveset and Zip files]]
 +
*[[Scanco_Administration#Backup_and_Archive| Backup and Archive]]
  
−
===Finite Element Modelling===
+
[[Scanco_Administration#Process.2C_Printer_and_System| '''Process, Printer and System''']]
−
----
+
*[[Scanco_Administration#Processes_and_Jobs| Processes and Jobs]]
−
*[[Tutorial on Generating AIMs for FE Analysis]]
+
*[[Scanco_Administration#Printer| Printer]]
−
: First steps for processing microCT data for FE analysis.
+
*[[Scanco_Administration#System| System]]
−
*[[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]]
 
−
: 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.
 
  
−
===Statistics===
+
[[Scanco_Administration#Remote_Access|'''Remote Access''']]
−
----
+
*[[Scanco_Administration#For_Scanco_support| For Scanco support]]
−
*[[JAGS Usage]]
+
*[[Scanco_Administration#Access_VMS_filesystem| Access VMS filesystem]]
−
: Analysis of Bayesian models using Markov Chain Monte Carlo
+
*[[Scanco_Administration#Setup_remote_access_FAQ| Setup remote access FAQ]]
 +
*[[Scanco_Administration#Physical_connections| Physical connections]]
  
−
===Computers===
+
[[Scanco_Administration#Dose| '''Dose''']]
−
----
+
*[[Scanco_Administration#Dose_Calculations| Dose Calculations]]
−
This section covers generic computer-related topics not covered in other sections.
+
*[[Scanco_Administration#Optimize_Scan_for_Low_Dose| Optimize Scan for Low Dose]]
−
*[[Unix command line basics]]
 
−
*[[ssh|Setting up Key Authentication for SSH]]
 
−
*[[Lab Server Configuration]]
 
  
 
|bgcolor="#CCCCCC"|
 
|bgcolor="#CCCCCC"|
 
|valign="top"|
 
|valign="top"|
  
−
===Developer===
+
==[[Xradia Instructions]]==
−
----
+
*[[Xradia_Instructions#User_Tutorials| User Tutorials]]
 +
*[[Xradia_Instructions#Scanning| Scanning]]
 +
*[[Xradia_Instructions#Reconstruction| Reconstruction]]
 +
*[[Xradia_Instructions#Special_Topics| Special Topics]]
 +
*[[Xradia_Instructions#Image_Tours| Image Tours]]
 +
 
 +
==[[Books and References]]==
 +
[[Books_and_References#Imaging|'''Imaging''']]
 +
*[[Books_and_References#Essential_Physics_of_Medical_Imaging| Essential Physics of Medical Imaging]]
 +
 
 +
[[Books_and_References#Bone|'''Bone''']]
 +
*[[Books_and_References#Books_on_Bone| Books on Bone]]
 +
*[[Books_and_References#Bone_Morphometry_and_Densitometry| Bone Morphometry and Densitometry]]
 +
 
 +
[[Books_and_References#Student_Reports|'''Student Reports''']]
  
−
====Lab Software Projects====
+
==[[Image Registration]]==
−
*[[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.
+
[[Image_Registration#Scanco_Image_Registration|'''Scanco Image Registration''']]
−
**[[vtkski development]]
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*[[Image_Registration#Image_Transformation|Image Transformation]]
−
**[[vtkMy development]]
+
*[[Image_Registration#Image_Registration|Image Registration]]
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*[[Bone lab applications]] provides a list of lab custom software.
+
*[[Image_Registration#Register_MRI_to_HR-pQCT|Register MRI to HR-pQCT]]
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*[[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 is a tool for visualizing and manipulating AIMs.
 
  
−
====Platforms====
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[[Image_Registration#Similarity_Registration|'''SimilarityRegistration''']]
−
Obtaining, compiling and installing software development tools on various systems.
+
*[[Image_Registration#Understand_rotation_parameters| Understand rotation parameters]]
−
*[[Development on OS-X]]
+
*[[Image_Registration#Set_optimizer_scales| Set optimizer scales]]
−
*[[Development for Linux]]
 
−
*[[Development on Windows]]
 
−
*[[Development on OpenVMS]]
 
  
−
====Languages and Toolkits====
+
[[Image_Registration#SkiRegistration|'''skiRegistration''']]
−
*[[C++ Development]]
+
*[[Image_Registration#ITK_Rigid_registration_for_HR-pQCT| ITK Rigid registration for HR-pQCT]]
−
*[[Creating VTK Classes]]
 
−
*[[ITK Development]]
 
  
−
====Development Tools====
+
==[[Finite Element Modelling]]==
−
*[[Subversion (SVN)]] for accessing the source code of lab software.
+
*[[Finite_Element_Modelling#Scanco_Finite_Element_Modelling| Scanco Finite Element Modelling]]
 +
*[[Finite_Element_Modelling#FAIM_Finite_Element_Solver| FAIM Finite Element Solver]]
 +
*[[Finite_Element_Modelling#FE_Tutorial| FE Tutorial]]
 +
*[[Finite_Element_Modelling#Prepare_AIMs_for_FE_Analysis| Prepare AIMs for FE Analysis]]
  
−
===Miscellaneous===
+
==[[Software Plugins and Codes]]==
 
----
 
----
−
*[[Wireless Network in Morphometrics Lab]]
+
*[[Software_Plugins_and_Codes#ImageJ| '''ImageJ''']]
−
*[[Archive]] Obsolete stuff here.
+
*[[Software_Plugins_and_Codes#Amira| '''Amira''']]
 +
*[[Software_Plugins_and_Codes#R|'''R''']]
 +
*[[Software_Plugins_and_Codes#ParaView| '''ParaView''']]
 +
 
 +
==Languages and Toolkits==
 +
*[[C++|'''C++''']]
 +
*[[VTK|'''VTK''']]
 +
*[[ITK|'''ITK''']]
 +
 
 +
==Miscellaneous==
 +
*[[Software_Development_Platforms| '''Software Development Platforms''']]
 +
*[[Archive|'''Archive''']]  
  
 
|}
 
|}
−
 
  
 
----
 
----
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<tr>
 
<tr>
 
<td align="left" valign="middle" >
 
<td align="left" valign="middle" >
−
A link back to: [http://www.enme.ucalgary.ca/~skboyd/ Steve Boyd's homepage]
+
To: [https://www.ucalgary.ca/labs/bonelab/team/steven-boyd '''Steve Boyd's homepage''']
 
</td>
 
</td>
−
<td align="left" valign="middle"> To return to the Lab home page: [http://www.enme.ucalgary.ca/research/microct/ Biomedical Imaging Metrics Homepage]</td>
+
<td align="left" valign="middle"> To: [https://www.ucalgary.ca/labs/bonelab/home '''Bone Imaging Lab homepage''']</td>
 
</tr></table>
 
</tr></table>

Latest revision as of 19:30, 5 May 2021

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.


The Purpose

It's to facilitate information exchange within the lab and keep up-to-date How To and User Manuals for lab's technical procedures and FAQ.
BonelabScanners.JPG
Read me

  1. Use Ctr+F to search within any page.
  2. Never include login credentials especially password anywhere.
  3. It's all users' responsibility to keep the info precise, updated, abundant, and useful, through editing/addition/deletion as needed by clicking [edit] on the top-right corner of a page or item. This includes combining same/similar topics besides an item whenever appropriate.
  4. Add a redirect line after each new item for consistency:
    Redirect.jpg Return to Contents or Return to Main Page
  5. Click Help on navigation list on the left penal for detailed editing instructions.
  6. Contact Ying if you are not sure where to put a new item or could not find an item.

Scanco User Instructions

OpenVMS Basics

Micro-CT Basics

Scanning

Evaluation

Results

Data Management

Import and Export

Remote Access

Scanco Administration

OpenVMS

Calibration and QC

Scanning

Evaluation

Results

Data Management

Process, Printer and System

Remote Access

Dose

Xradia Instructions

Books and References

Imaging

Bone

Student Reports

Image Registration

Scanco Image Registration

SimilarityRegistration

skiRegistration

Finite Element Modelling

Software Plugins and Codes

Languages and Toolkits

Miscellaneous

To: Steve Boyd's homepage

To: Bone Imaging Lab homepage
Retrieved from "http://bone.wiki/index.php?title=Main_Page&oldid=7123"