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__NOTOC__ <center><b><font size="+3">Bone Imaging Laboratory Wiki</font></b> <table width="100%" border="0"> <tr> <td width="15%" align="center" valign="middle" bgcolor="#ccff66"> <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> <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> </tr> </table> </center> {| border="0" align="center" width="98%" valign="top" cellspacing="7" cellpadding="2" |- ! width="33%"| ! | ! width="33%"| ! | ! width="33%"| |- |valign="top"| ==[[Scanco User Instructions]]== [[Scanco_User_Instructions#OpenVMS_Basics| '''OpenVMS Basics''']] *[[Scanco_User_Instructions#OpenVMS_Beginner.27s_Reference| Beginner's Reference]] *[[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#DCL_Programming_Guide| DCL Programming Guide]] *[[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| 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"| |valign="top"| ==[[Scanco Administration]]== [[Scanco_Administration#OpenVMS| '''OpenVMS''']] *[[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]] [[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#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]] [[Scanco_Administration#Remote_Access|'''Remote Access''']] *[[Scanco_Administration#For_Scanco_support| For Scanco support]] *[[Scanco_Administration#Access_VMS_filesystem| Access VMS filesystem]] *[[Scanco_Administration#Setup_remote_access_FAQ| Setup remote access FAQ]] *[[Scanco_Administration#Physical_connections| Physical connections]] [[Scanco_Administration#Dose| '''Dose''']] *[[Scanco_Administration#Dose_Calculations| Dose Calculations]] *[[Scanco_Administration#Optimize_Scan_for_Low_Dose| Optimize Scan for Low Dose]] |bgcolor="#CCCCCC"| |valign="top"| ==[[Opportunistic CT]]== [[Opportunistic_CT#Radiation_Dose|'''Radiation Dose''']] *[[Opportunistic_CT#Dose_Length_Product|Dose Length Product]] *[[Opportunistic_CT#Effective_Dose|Effective Dose]] [[Opportunistic_CT#Calibration|'''Calibration''']] *[[Opportunistic_CT#Phantom_calibration | Phantom]] *[[Opportunistic_CT#Asynchronous_calibration |Asynchronous]] *[[Opportunistic_CT#Internal_calibration| Internal]] ==[[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#ImageJ| '''ImageJ''']] *[[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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