Editing Archive (section)

===HowTo: Select a threshold===

:* Should be as deep a threshold possible without creating fragments.
:* Threshold given as a value between 1 and 1000.
:* A common value is 224 of a possible 1000 (22.4%).
:* Work with a representative sub-aim (see HowTo:) approximately 100 voxels cubed.
:<I>Option 1: Mcubes and Viza</I>
:* Select the threshold after ensuring there aren’t too many fragments.
:* Note that the value given here is twice the threshold value that should be used. For some reason, if you choose 40% threshold in <code>mcubes</code>, that number corresponds to a real threshold (for use in IPL commands) of 20% or 200.
:<I>Option 2: SAP</I>
:* Read in the Gaussian filtered aim [<code>Processing:segmentation:procedures</code>].
:* Threshold<I> only</I>.
:* With different thresholds, switch between the original data and the thresholded data until satisfactory. Try other planes too!
:* Go to maximum threshold until bonds are broken.