Editing Scanco User Instructions (section)

==Evaluation Scripts==
===Scanco Standard Evaluation Scripts===
The following are descriptions of some of the standard evaluation scripts provided by Scanco Medical.  

*'''3D Segmentation of VOI, 1 solid object'''
:Produces a 3D segmented (binary) object with values 0 (background, hidden) and 127 (solid).  Input Gaussian filtering and threshold parameters.  Draw contour to isolate the object of interest (optional).

*'''3D Seg. of 2 VOIs: solid dense in transparent low dens obj'''
:Produces a 3D segmented object with values -1 (transparent), 0 (background, hidden), and 127 (solid). Input two sets of Gaussian filtering and threshold parameters (input the second set by pressing the red 2 button).  The preview shows the solid object in white and the transparent object in red.  Draw one contour to isolate the object of interest (optional).  This script is useful for showing soft tissue and bone.

*'''Bone Trab. Morphometry (3D Seg, 3D Calc, Print Sheet)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs.   Draw contour to isolate the trabecular bone.  Performs model-independent (direct) measurements on the trabecular region.  Outputs:  BV, TV, BV/TV, TbBMD, TbTMD, BS, SMI, DA, ConnD, TbTh, TbThSD, TbSp, TbSpSD, TbN, and Tb1/NSD.

*'''BV/Density only Bone Eval. (3D Seg, BV and Dens Calc, Print)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs.   Draw contour to isolate the region of interest.  Outputs:  BV, TV, BV/TV, BMD, and TMD.

*'''Bone Midshaft Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs.   Draw contour on the outer surface of the bone.  Outputs:  BV, TV, BV/TV, BMD, TMD, and moment of inertia parameters.

*'''Bone Midshaft more than e.g. 50 slices Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs.   Draw contour on the outer surface of the bone.  If you wish to exclude the medullary area from the analysis, then draw a counterclockwise contour on the outer surface of the bone and a clockwise contour on the inner surface of the bone.  Performs direct measurements in addition to the standard midshaft analysis.  Outputs:  BV, TV, BV/TV, BMD, TMD, moment of inertia parameters, Th, and Sp.

*'''Convert to TIFF'''
:Converts the grayscale data to TIFF slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Convert to DICOM'''
:Converts the grayscale data to DICOM slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Reformat to Axial Cuts'''
:Flips the dataset from the XY plane to the XZ or YZ planes (specify in the advanced options for the script). This is useful if you want to contour your sample in a different plane.  The flipped sample is imported as a new measurement under the same sample number as the original data.


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===Understanding Evaluation Scripts===
Following are some example evaluation scripts full of comments to promote understanding:
*[[Media:IPLV6_VOI.pdf|IPLV6_VOI script]]
*[[Media:IPLV6_MIDSHAFT.pdf|IPLV6_MIDSHAFT script]]
*[[Media:IPLV6_TRABECULAR_BONE.pdf|IPLV6_TRABECULAR_BONE script]]


===Setup Customized Evaluation Scripts===
To setup an evaluation script customized to your project, in the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']]:
*Choose "Scripts" then "Import from" then "TEMPLATES", pick a Scanco Standard Evaluation Scripts and Save.  
*Choose "Scripts" then "Modify".  Choose the script that was just imported and click "OK",  Change the name of the script.  
*Modify the default segmentation and other parameters for the script.  When finished making changes press "Save" then "OK".


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