Difference between revisions of "Main Page"

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__NOTOC__
 
__NOTOC__
 
 
<center><b><font size="+3">Bone Imaging Laboratory Wiki</font></b>
 
<center><b><font size="+3">Bone Imaging Laboratory Wiki</font></b>
 
  
  
 
<table width="97%" border="0">
 
<table width="97%" border="0">
 
<tr>  
 
<tr>  
<td width="450" align="left" valign="middle" bgcolor="#ccff66">
+
<td width="200" 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> <br>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
+
 
information exchange within the lab and keep up-to-date How To and User Manuals for all lab procedures.</P>
+
</td>
 +
 
 +
<td bgcolor="#ccff66">      [[File:BonelabScanners.JPG|center|700px]]</td>
 +
 
 +
<td width="200" align="center" valign="middle" bgcolor="#ccff66">
 +
<div align="center"><b><u> The Purpose</u></b></div>
 +
 
 +
<p><br>It's to facilitate information exchange within the lab and keep up-to-date How To and User Manuals for all lab procedures.</P>
 
</td>
 
</td>
  
<td bgcolor="#ccff05">[[Image:Smaller_bone_loss.jpg]]</td>
 
 
</tr>
 
</tr>
 
</table>
 
</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]]===
+
==[[Scanco User Instructions]]==
----
+
[[Scanco_User_Instructions#OpenVMS_Basics| '''OpenVMS Basics''']]
*[[Scanco_User_Instructions#OpenVMS_Basics| '''OpenVMS Basics''']]
+
*[[Scanco_User_Instructions#OpenVMS_Beginner.27s_Reference| Beginner's Reference]]
**[[Scanco_User_Instructions#OpenVMS_Beginner.27s_Reference| Beginner's Reference]]
+
*[[Scanco_User_Instructions#Session_Manager| Session Manager]]
**[[Scanco_User_Instructions#Session_Manager| Session Manager]]
+
*[[Scanco_User_Instructions#DEC_Terminal_and_Digital_Command_Language_.28DCL.29| DEC Terminal and DCL]]
**[[Scanco_User_Instructions#DEC_Terminal_and_Digital_Command_Language_.28DCL.29| DEC Terminal and DCL]]
+
*[[Scanco_User_Instructions#DCL_Programming_Guide| DCL Programming Guide]]
**[[Scanco_User_Instructions#DCL_Programming_Guide| DCL Programming Guide]]
+
*[[Scanco_User_Instructions#List_of_basic_commands| List of basic commands]]
**[[Scanco_User_Instructions#List_of_basic_commands| List of basic commands]]
 
 
 
*[[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_Type| Image Data Type]]
 
**[[Scanco_User_Instructions#Scanco_Medical_Micro-CT_Software| Scanco Medical µCT Software]]
 
 
 
*[[Scanco_User_Instructions#Bone_Morphometry_and_Densitometry| '''Bone Morphometry and Densitometry''']]
 
**[[Scanco_User_Instructions#Suggested_readings| Suggested readings]]
 
**[[Scanco_User_Instructions#Model-Independent_.28Direct.29_Structural_Measurements| Model-Independent (Direct) Structural Measurements]]
 
**[[Scanco_User_Instructions#Densitometric_Measurements| Densitometric Measurements]]
 
  
*[[Scanco_User_Instructions#Scanning| '''Scanning''']]
+
[[Scanco_User_Instructions#Micro-Computed_Tomography_.28.C2.B5CT.29_Basics| '''Micro-CT Basics''']]
**[[Scanco_User_Instructions#Sample_Name_Convention| Sample Name Convention]]
+
*[[Scanco_User_Instructions#User_Tutorials| User Tutorials]]
**[[Scanco_User_Instructions#Register_Samples_for_Scanning| Register Samples for Scanning]]
+
*[[Scanco_User_Instructions#Micro-CT_Image_Basics| µCT Image Basics]]
**[[Scanco_User_Instructions#Log_Sheets| Log Sheets]]
+
*[[Scanco_User_Instructions#Image_Data| Image Data]]
**[[Scanco_User_Instructions#Patient_Casts_and_Sample_Holders| Patient Casts and Sample Holders]]
+
*[[Scanco_User_Instructions#Scanco_Medical_Micro-CT_Software| Scanco Medical µCT Software]]
**[[Scanco_User_Instructions#Scan_Parameters_.28Controlfiles.29| Scan Parameters (Controlfiles)]]
 
**[[Scanco_User_Instructions#Perform_a_Scan| Perform a Scan]]
 
**[[Scanco_User_Instructions#Image_Artifacts| Image Artifacts]]
 
  
*[[Scanco_User_Instructions#Evaluation| '''Evaluation''']]
+
[[Scanco_User_Instructions#Scanning| '''Scanning''']]
**[[Scanco_User_Instructions#Evaluate_a_Scan| Evaluate a Scan]]
+
*[[Scanco_User_Instructions#Sample_Name_Convention| Sample Name Convention]]
**[[Scanco_User_Instructions#Draw_Contours| Draw Contours]]
+
*[[Scanco_User_Instructions#Register_Samples_for_Scanning| Register Samples for Scanning]]
**[[Scanco_User_Instructions#Evaluation_Scripts| Evaluation Scripts]]
+
*[[Scanco_User_Instructions#Log_Sheets| Log Sheets]]
**[[Scanco_User_Instructions#Image_Processing_Language_.28IPL.29_Scripting| IPL Scripting]]
+
*[[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#Results| '''Results''']]
+
[[Scanco_User_Instructions#Evaluation| '''Evaluation''']]
**[[Scanco_User_Instructions#Extract_Results| Extract Results]]
+
*[[Scanco_User_Instructions#Evaluate_a_Scan| Evaluate a Scan]]
**[[Scanco_User_Instructions#Generate_Report| Generate Report]]
+
*[[Scanco_User_Instructions#Draw_Contours| Draw Contours]]
**[[Scanco_User_Instructions#Result_Analysis_Script| Result Analysis Script]]
+
*[[Scanco_User_Instructions#Evaluation_Scripts| Evaluation Scripts]]
**[[Scanco_User_Instructions#Images_and_Animations| Images and Animations]]
+
*[[Scanco_User_Instructions#Image_Processing_Language_.28IPL.29_Scripting| IPL Scripting]]
  
*[[Scanco_User_Instructions#Backup_and_Deletion| '''Backup and Deletion''']]
+
[[Scanco_User_Instructions#Results| '''Results''']]
**[[Scanco_User_Instructions#Trainee.E2.80.99s_Data_Responsibility| Trainee’s Data Responsibility]]
+
*[[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#Export_and_Import| '''Export and Import''']]
+
[[Scanco_User_Instructions#Data_Management| '''Data Management''']]
**[[Scanco_User_Instructions#Get_Your_Files| Get Your Files]]
+
*[[Scanco_User_Instructions#Trainee.E2.80.99s_Data_Responsibility| Trainee’s Data Responsibility]]
**[[Scanco_User_Instructions#Import_MRI_to_Scanco_System| Import MRI Images]]
+
*[[Scanco_User_Instructions#Move_data_from_Data_Disk_to_Project_Disk| Move data from Data Disk to Project Disk]]
**[[Scanco_User_Instructions#Import_Xradia_.2A.bin_to_Scanco_System|Import Xradia *.bin]]
 
  
*[[Scanco_User_Instructions#Remote_Access| '''Remote Access''']]
+
[[Scanco_User_Instructions#Import_and_Export| '''Import and Export''']]
**[[Scanco_User_Instructions#VPN_Setup| VPN Setup]]
+
*[[Scanco_User_Instructions#Import_Foreign_Data_to_Scanco_System| Import Foreign Data]]
**[[Scanco_User_Instructions#Setup_for_MAC.2FLinux| Setup for MAC/Linux]]
+
*[[Scanco_User_Instructions#Import_MRI_to_Scanco_System| Import MRI Images]]
**[[Scanco_User_Instructions#Setup_for_Windows| Setup for Windows]]
+
*[[Scanco_User_Instructions#Import_Xradia_.2A.bin_to_Scanco_System|Import Xradia *.bin]]
**[[Scanco_User_Instructions#Remote_Access_FAQ| Remote Access FAQ]]
+
*[[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]]===
+
==[[Scanco Administration]]==
----
+
[[Scanco_Administration#OpenVMS| '''OpenVMS''']]
* [[Scanco_Administration#OpenVMS| '''OpenVMS''']]
+
*[[Scanco_Administration#OpenVMS_References| OpenVMS References]]
**[[Scanco_Administration#OpenVMS_References| OpenVMS References]]
+
*[[Scanco_Administration#Unix_related| Unix related]]
**[[Scanco_Administration#Unix_related| Unix related]]
+
*[[Scanco_Administration#Graphical_Applications| Graphical Applications]]
**[[Scanco_Administration#Graphical_Applications| Graphical Applications]]
+
*[[Scanco_Administration#File_Operations| File Operations]]
**[[Scanco_Administration#File_Operation| File Operation]]
+
*[[Scanco_Administration#Administrative_Commands| Administrative Commands]]
**[[Scanco_Administration#Administrative_Commands| Administrative Commands]]
 
  
* [[Scanco_Administration#Calibration_and_QC | '''Calibration and QC''']]
+
[[Scanco_Administration#Calibration_and_QC | '''Calibration and QC''']]
**[[Scanco_Administration#System_Updates| System Updates]]
+
*[[Scanco_Administration#System_Updates| System Updates]]
**[[Scanco_Administration#Calibration_and_Conversion| Calibration and Conversion]]
+
*[[Scanco_Administration#Calibration_and_Conversion| Calibration and Conversion]]
**[[Scanco_Administration#Quality_Control_.28QC.29| Quality Control (QC)]]
+
*[[Scanco_Administration#Quality_Control_.28QC.29| Quality Control (QC)]]
  
* [[Scanco_Administration#Scanning_FAQ| '''Scanning FAQ''']]
+
[[Scanco_Administration#Scanning| '''Scanning''']]
**[[Scanco_Administration#Scanner_User_Manual| Scanner User Manual]]
+
*[[Scanco_Administration#Scanner_User_Manual| Scanner User Manual]]
**[[Scanco_Administration#Scanco.27s_FAQ| Scanco's FAQ]]
+
*[[Scanco_Administration#Scanco.27s_FAQ| Scanco's FAQ]]
**[[Scanco_Administration#Reconstruction| Reconstruction]]
+
*[[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#Data_Management | '''Data Management''']]
+
[[Scanco_Administration#Evaluation| '''Evaluation''']]
**[[Scanco_Administration#Lab.E2.80.99s_Data_Responsibility| Lab’s Data Responsibility]]
+
*[[Scanco_Administration#Analysis_Topics| Analysis Topics]]
**[[Scanco_Administration#Tape| Tape]]
+
*[[Scanco_Administration#UCT_EVALUATION| UCT_EVALUATION]]
**[[Scanco_Administration#USB_Drive| USB_Drive]]
+
*[[Scanco_Administration#Evaluation_FAQ| Evaluation FAQ]]
**[[Scanco_Administration#CDROM| CDROM]]
+
*[[Scanco_Administration#IPL_FAQ| IPL FAQ]]
**[[Scanco_Administration#Saveset_and_Zip_files| Saveset and Zip files]]
 
**[[Scanco_Administration#Backup_and_Archive| Backup and Archive]]
 
  
* [[Scanco_Administration#Process.2C_Printer_and_System| '''Process, Printer and System''']]
+
[[Scanco_Administration#Results| '''Results''']]
**[[Scanco_Administration#Processes_and_Jobs| Processes and Jobs]]
+
*[[Scanco_Administration#Extract_Results| Extract Results]]
**[[Scanco_Administration#Printer| Printer]]
+
*[[Scanco_Administration#Database| Database]]
**[[Scanco_Administration#System| System]]
+
*[[Scanco_Administration#Other_FAQ| Other FAQ]]
  
*[[Scanco_Administration#Remote_Access_2|'''Remote Access''']]
+
[[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]]
  
*[[Scanco_Administration#Dose| '''Dose''']]
+
[[Scanco_Administration#Process.2C_Printer_and_System| '''Process, Printer and System''']]
 +
*[[Scanco_Administration#Processes_and_Jobs| Processes and Jobs]]
 +
*[[Scanco_Administration#Printer| Printer]]
 +
*[[Scanco_Administration#System| System]]
  
===Registration and Segmentation===
+
[[Scanco_Administration#Remote_Access|'''Remote Access''']]
----
+
*[[Scanco_Administration#For_Scanco_support| For Scanco support]]
*[[Scanco Image Registration]]
+
*[[Scanco_Administration#Access_VMS_filesystem| Access VMS filesystem]]
*[[SimilarityRegistration]]
+
*[[Scanco_Administration#Setup_remote_access_FAQ| Setup remote access FAQ]]
*[[skiRegistration]]
+
*[[Scanco_Administration#Physical_connections| Physical connections]]
*[[MRI to HR-pQCT Registration with Scanco]]
 
  
===Finite Element Modelling===
+
[[Scanco_Administration#Dose| '''Dose''']]
----
+
*[[Scanco_Administration#Dose_Calculations| Dose Calculations]]
*[[FAIM Finite Element Solver]]
+
*[[Scanco_Administration#Optimize_Scan_for_Low_Dose| Optimize Scan for Low Dose]]
: 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.
 
 
 
===Computers===
 
----
 
This section covers generic computer-related topics not covered in other sections.
 
*[[Unix command line basics]]
 
*[[ssh|SSH tricks]]
 
*[[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''']]
 +
 
 +
==[[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]]
 +
 
 +
==[[Finite Element Modelling]]==
 +
*[[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]]
  
====[[Software Plugins and Codes]]====
+
==[[Software Plugins and Codes]]==
 
----
 
----
* [[Software_Plugins_and_Codes#ImageJ_Plugin_for_AIM_ISQ_RSQ_files| ImageJ Plugin for AIM ISQ RSQ files]]
+
*[[Software_Plugins_and_Codes#ImageJ| '''ImageJ''']]
* [[Software_Plugins_and_Codes#Amira_Script_for_AIM_files| Amira Script for AIM files]]
+
*[[Software_Plugins_and_Codes#Amira| '''Amira''']]
*[[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.
+
*[[Software_Plugins_and_Codes#R|'''R''']]  
*[[Bone lab applications]] provides a list of lab custom software.
+
*[[Software_Plugins_and_Codes#ParaView| '''ParaView''']]
*[[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====
+
==Languages and Toolkits==
----
+
*[[C++|'''C++''']]
Obtaining, compiling and installing software development tools on various systems.
+
*[[VTK|'''VTK''']]
*[[Development on OS-X]]
+
*[[ITK|'''ITK''']]
*[[Development for Linux]]
 
*[[Development on Windows]]
 
*[[Development on OpenVMS]]
 
  
====Languages and Toolkits====
+
==Miscellaneous==
----
+
*[[Software_Development_Platforms| '''Software Development Platforms''']]
*[[C++ Development]]
+
*[[Archive|'''Archive''']]  
*[[Creating VTK Classes]]
 
*[[ITK Development]]
 
*[[Matlab Development]]
 
*[[Writing plugins for ParaView]]
 
  
===Miscellaneous===
 
----
 
*[[Wireless Network in Morphometrics Lab]]
 
*[[Archive]] Obsolete stuff here.
 
* [[Project Management]]
 
* [[Scanco MicroCT Operation]]
 
* [[MicroCT Evaluation and Analysis]]
 
* [[Writing IPL Scripts]]
 
* [[Errors and Fixes]]
 
 
|}
 
|}
 
  
 
----
 
----
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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>

Revision as of 16:02, 22 January 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. Also, there is a document section where useful documents can uploaded or downloaded by anyone in the group.

BonelabScanners.JPG
The Purpose


It's to facilitate information exchange within the lab and keep up-to-date How To and User Manuals for all lab procedures.

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