Editing Scanco Administration (section)

====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