Editing Scanco Administration (section)

====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.