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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">
<table width="97%" border="0">
 
 
<tr>  
 
<tr>  
<td width="450" align="left" valign="middle" bgcolor="#ccff66">
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<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
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<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>
 +
 
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</td>
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<td bgcolor="#ccff66">      [[File:BonelabScanners.JPG|center|750px]]</td>
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<td width="25%" align="left" valign="middle" bgcolor="#ccff66">
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<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>
  
<td bgcolor="#ccff05">[[Image:Smaller_bone_loss.jpg]]</td>
 
 
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</table>
 
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</center>
 
</center>
  
== 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"|
  
===[[Scanco User Instructions]]===
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==[[Scanco User Instructions]]==
----
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[[Scanco_User_Instructions#OpenVMS_Basics| '''OpenVMS Basics''']]
* [http://bone.wiki/index.php?title=Scanco_User_Instructions#OpenVMS_Basics OpenVMS Basics]
+
*[[Scanco_User_Instructions#OpenVMS_Beginner.27s_Reference| Beginner's Reference]]
* [http://bone.wiki/index.php?title=Scanco_User_Instructions#Scanning Scanning]
+
*[[Scanco_User_Instructions#Session_Manager| Session Manager]]
* [[Project Management]]
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*[[Scanco_User_Instructions#DEC_Terminal_and_Digital_Command_Language_.28DCL.29| DEC Terminal and DCL]]
* [[Scanco MicroCT Operation]]
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*[[Scanco_User_Instructions#DCL_Programming_Guide| DCL Programming Guide]]
* [[MicroCT Evaluation and Analysis]]
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*[[Scanco_User_Instructions#List_of_basic_commands| List of basic commands]]
* [[Writing IPL Scripts]]
+
 
* [[Errors and Fixes]]
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[[Scanco_User_Instructions#Micro-Computed_Tomography_.28.C2.B5CT.29_Basics| '''Micro-CT Basics''']]
* [[Uploading MRI to Scanco]]
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*[[Scanco_User_Instructions#User_Tutorials| User Tutorials]]
* [[Uploading Xradia *.bin to Scanco]]
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*[[Scanco_User_Instructions#Micro-CT_Image_Basics| µCT Image Basics]]
* [[Remote Access (working from home)]]
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*[[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]]
 +
 
 +
[[Scanco_User_Instructions#Import_and_Export| '''Import and Export''']]
 +
*[[Scanco_User_Instructions#Import_Foreign_Data_to_Scanco_System| Import Foreign Data]]
 +
*[[Scanco_User_Instructions#Import_MRI_to_Scanco_System| Import MRI Images]]
 +
*[[Scanco_User_Instructions#Import_Xradia_.2A.bin_to_Scanco_System|Import Xradia *.bin]]
 +
*[[Scanco_User_Instructions#Get_Your_Files| Get Your Files]]
  
 +
[[Scanco_User_Instructions#Remote_Access| '''Remote Access''']]
 +
*[[Scanco_User_Instructions#VPN_Setup| VPN Setup]]
 +
*[[Scanco_User_Instructions#Setup_for_MAC.2FLinux| Setup for MAC/Linux]]
 +
*[[Scanco_User_Instructions#Setup_for_Windows| Setup for Windows]]
 +
*[[Scanco_User_Instructions#Remote_Access_FAQ| Remote Access FAQ]]
  
 
|bgcolor="#CCCCCC"|
 
|bgcolor="#CCCCCC"|
 
|valign="top"|
 
|valign="top"|
  
===[[Scanco Administration]]===
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==[[Scanco Administration]]==
----
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[[Scanco_Administration#OpenVMS| '''OpenVMS''']]
* [http://bone.wiki/index.php?title=Scanco_Administration#OpenVMS OpenVMS]
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*[[Scanco_Administration#OpenVMS_References| OpenVMS References]]
* [http://bone.wiki/index.php?title=OpenVMS#Scanning_FAQ Scanning FAQ]
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*[[Scanco_Administration#Unix_related| Unix related]]
* [[Reconstruction]]
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*[[Scanco_Administration#Graphical_Applications| Graphical Applications]]
* [[Process, Jobs and Printing]]
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*[[Scanco_Administration#File_Operations| File Operations]]
* [[Data Management]]
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*[[Scanco_Administration#Administrative_Commands| Administrative Commands]]
* [[Remote Access]]
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* [[Calibration]]
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[[Scanco_Administration#Calibration_and_QC | '''Calibration and QC''']]
* [[Dose]]
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*[[Scanco_Administration#System_Updates| System Updates]]
* [[Software FAQ]]
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*[[Scanco_Administration#Calibration_and_Conversion| Calibration and Conversion]]
* [[Hardware FAQ]]
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*[[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]]
 +
 
 +
[[Scanco_Administration#Data_Management | '''Data Management''']]
 +
*[[Scanco_Administration#Lab.E2.80.99s_Data_Responsibility| Lab’s Data Responsibility]]
 +
*[[Scanco_Administration#HP_Server_and_Disk_Array| HP Server and Disk Array]]
 +
*[[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]]
  
===Registration and Segmentation===
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[[Scanco_Administration#Process.2C_Printer_and_System| '''Process, Printer and System''']]
----
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*[[Scanco_Administration#Processes_and_Jobs| Processes and Jobs]]
*[[Scanco Image Registration]]
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*[[Scanco_Administration#Printer| Printer]]
*[[SimilarityRegistration]]
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*[[Scanco_Administration#System| System]]
*[[skiRegistration]]
 
*[[MRI to HR-pQCT Registration with Scanco]]
 
  
===Finite Element Modelling===
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[[Scanco_Administration#Remote_Access|'''Remote Access''']]
----
+
*[[Scanco_Administration#For_Scanco_support| For Scanco support]]
*[[FAIM Finite Element Solver]]
+
*[[Scanco_Administration#Access_VMS_filesystem| Access VMS filesystem]]
: This is the lab finite element software.
+
*[[Scanco_Administration#Setup_remote_access_FAQ| Setup remote access FAQ]]
*[[Tutorial on Generating AIMs for FE Analysis]]
+
*[[Scanco_Administration#Physical_connections| Physical connections]]
: 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.
 
  
===Computers===
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[[Scanco_Administration#Dose| '''Dose''']]
----
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*[[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|SSH tricks]]
 
*[[Lab Server Configuration]]
 
  
 
|bgcolor="#CCCCCC"|
 
|bgcolor="#CCCCCC"|
 
|valign="top"|
 
|valign="top"|
  
===Developer===
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==[[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''']]
 +
 
 +
==[[Image Registration]]==
 +
[[Image_Registration#Scanco_Image_Registration|'''Scanco Image Registration''']]
 +
*[[Image_Registration#Image_Transformation|Image Transformation]]
 +
*[[Image_Registration#Image_Registration|Image Registration]]
 +
*[[Image_Registration#Register_MRI_to_HR-pQCT|Register MRI to HR-pQCT]]
 +
 
 +
[[Image_Registration#Similarity_Registration|'''SimilarityRegistration''']]
 +
*[[Image_Registration#Understand_rotation_parameters| Understand rotation parameters]]
 +
*[[Image_Registration#Set_optimizer_scales| Set optimizer scales]]
 +
 
 +
[[Image_Registration#SkiRegistration|'''skiRegistration''']]
 +
*[[Image_Registration#ITK_Rigid_registration_for_HR-pQCT| ITK Rigid registration for HR-pQCT]]
  
====Software and Plugins====
+
==[[Finite Element Modelling]]==
----
+
*[[Finite_Element_Modelling#Scanco_Finite_Element_Modelling| Scanco Finite Element Modelling]]
*[[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.
+
*[[Finite_Element_Modelling#FAIM_Finite_Element_Solver| FAIM Finite Element Solver]]
*[[Bone lab applications]] provides a list of lab custom software.
+
*[[Finite_Element_Modelling#FE_Tutorial| FE Tutorial]]
*[[SAP development]]
+
*[[Finite_Element_Modelling#Prepare_AIMs_for_FE_Analysis| Prepare AIMs for FE Analysis]]
: 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====
+
==[[Software Plugins and Codes]]==
 
----
 
----
Obtaining, compiling and installing software development tools on various systems.
+
*[[Software_Plugins_and_Codes#ImageJ| '''ImageJ''']]
*[[Development on OS-X]]
+
*[[Software_Plugins_and_Codes#Amira| '''Amira''']]
*[[Development for Linux]]
+
*[[Software_Plugins_and_Codes#R|'''R''']]  
*[[Development on Windows]]
+
*[[Software_Plugins_and_Codes#ParaView| '''ParaView''']]
*[[Development on OpenVMS]]
 
  
====Languages and Toolkits====
+
==Languages and Toolkits==
----
+
*[[C++|'''C++''']]
*[[C++ Development]]
+
*[[VTK|'''VTK''']]
*[[Creating VTK Classes]]
+
*[[ITK|'''ITK''']]
*[[ITK Development]]
 
*[[Matlab Development]]
 
*[[Writing plugins for ParaView]]
 
  
===Miscellaneous===
+
==Miscellaneous==
----
+
*[[Software_Development_Platforms| '''Software Development Platforms''']]
*[[Wireless Network in Morphometrics Lab]]
+
*[[Archive|'''Archive''']]  
*[[Archive]] Obsolete stuff here.
 
  
 
|}
 
|}
 
  
 
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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 18:30, 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