Editing Scanco Administration (section)

===Cortical porosity and finite element analysis on XtremeCT===

* This procedure is broken down into 3 separate components
* All Scripts mentioned be copied directly from DISK3:[MICROCT.PROJECTS.KYLE.SCRIPTS]
* Files should be copied from data to projects prior to running analysis (see bonelab procedures.doc on sodor) 

1. Autocontour the image <br>
2. Calculate and extract cortical measurements <br>
3. Create FE files and run FE <br>


====Autocontour====
* The main autocontour script is located in the ue: directory, this should NOT be modified!
* The procedure is executed using a "hijack" script [[Media:HIJACK_AUTOCONTOUR.TXT|'''HIJACK_AUTOCONTOUR.TXT''']], but the filename must be changed to .COM or found in the directory mentioned above.
* Files should already have a _SEG.AIM created and should be in the same directory as the raw .AIM file.

* You then create a SUBMIT.COM script as you would for other files. For example:
 $  QQ = "SUBMIT/NOPRINT/QUE=SCEVAL_FAST/LOG=SYS$SCRATCH com:HIJACK_AUTOCONTOUR.COM"
 $ 'QQ' /PARA=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.MODELS]'''FILENAME'''.AIM

* This command will then create various files for examination and further analysis. These include:
** FILENAME_COMBI.AIM - shows cortical, trabecular, and pores all in different colors
** FILENAME_COMBIPO.AIM - shows only the cortex with porosity as different color
** FILENAME_CRTXFILL.AIM - gives sold mask of cortex, porosity filled (can be used to calculate Ct.Th)
** FILENAME_CRTXPO.AIM - shows only the pores
** FILENAME_TRAB.GOBJ - gobj of trabecular region
** FILENAME_CRTX.GOBJ - gobj of cortical region
** FILENAME_AUTO2.GOBJ - gobj of whole bone region

* Further technical details and references can be found in the following publications:
** Buie, H., Campbell, G., Klinck, R., MacNeil, J., & Boyd, S. (2007). Automatic segmentation of cortical and trabecular compartments based on a dual threshold technique for in vivo micro-CT bone analysis. Bone, 41(4), 505-515. 
** K.K. Nishiyama, Macdonald, H., Buie, H., Hanley, D., & Boyd, S. (2010). Postmenopausal Women With Osteopenia Have Higher Cortical Porosity and Thinner Cortices at the Distal Radius and Tibia Than Women With Normal aBMD: An In Vivo HR-pQCT Study. Journal of Bone and Mineral Research, 25(4), 882-890.

====Evaluate Cortex====

*This Step 2 method of doing the cortical analysis is no longer used now that we have the IPL_UPAT_CALGARY_EVAL_XT1.COM or XT2.COM version. The problem with this approach is that it is a Frankenstein of the standard analysis and the advanced analysis. The cortical bone assessment is correct, but the trabecular compartment from the standard analysis is not a perfect match. Instead, we should be using the GOBJs described in IPL_UPAT_CALGARY_EVAL_XT1.COM so that we have a perfect mix. 
  
Nevertheless, we keep this information here for now for posterity.


*After the autocontour is computed we used to call IPL_EVAL_CORTEX.COM that will calculate the cortical parameters:
**Cortical porosity (%)
**Direct cortical thickness (mm)
**Cortical density (mg HA/ccm)

This WAS called as the following:
 $  QQ = "SUBMIT/NOPRINT/QUE=SCEVAL_FAST/LOG=SYS$SCRATCH com:IPL_EVAL_CORTEX.COM"
 $ 'QQ' /PARA=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.MODELS]'''FILENAME.AIM''' -
        /LOG=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.LOG]'''FILENAME'''_EVAL_CRTX.LOG


* The results of this script are outputed into individual log files for each file being evaluated.
* To extract these results into one file use:
 $ search/output=output_results_filename.txt *EVAL_CRTX.LOG "!% ov/tv","!> C.Th","!% mean_unit"
*A learn command in the eve editor can be used to extract the specific results desired:
**!% ov/tv is the amount of bone in the cortex (ie. 1- ov/tv =  cortical porosity)
**!> C.Th is the direct cortical thickness in mm
**!% mean_unit is the cortical density in mg HA/ccm

====Create and run FE models====

*The most current common FE model to run is a homogeneous model where all elements have the same material properties and the cortex and trabecular regions are labeled separately in order to determine the percentage of load carried by each region.
*The other option is to create a model where the material properties are scaled based on the density values and scripts for this can be found in the COM directory.

*The script IPL_FEM_HOMOGEMOUS_LS.COM will use files created by the autocontour and appropriately label the cortex and trabecular regions as well as remove any disconnected pieces of bone.
 $  QQ = "SUBMIT/NOPRINT/QUE=SCEVAL_FAST/LOG=SYS$SCRATCH com:IPL_FEM_HOMOGENOUS_LS.COM"
 $ 'QQ' /PARA=DISK3:[MICROCT.PROJECTS.'''PROJECT_NAME'''.MODELS]'''FILENAME'''.AIM

*Files will now be created with the suffix _HOM_LS.AIM and can be moved to Mighty-Mac or Mavis for FE analysis.  You will require user accounts for these computers and can contact Eric or Steve. If using FTP be sure to transfer the files in binary mode (further documentation on this can be found in this Wiki)

*[[Media:2009-10-15_FEM_Tutorial.pdf|'''FEM tutorial main steps''']] to submit the FE files with a detailed manual is recommended for first time users.
*This is now out of date, but is kept here because it still contains useful information about preparing AIM files and post-processing.  
*For running the FE itself, please refer to the current manual at [[FAIM Finite Element Solver]].


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