[vtkusers] High memory cost of vtkDecimatePro for 3D model generation from DICOM series

[Liu_tj]

Hi, David,

Thanks for your detail reply.

I thought that vtkImageThreshold still provide a greyscale output instead of binary output. My understanding was that vtkImageThreshold just remove the points beyond the greyscale range.


Thanks
Liu Peng



在2016-03-18，"David Gobbi" <david.gobbi at gmail.com> 写道： -----原始邮件-----
发件人:"David Gobbi" <david.gobbi at gmail.com>
发送时间:2016年03月18日 星期五
收件人:"Elvis Stansvik" <elvis.stansvik at orexplore.com>
抄送:"Liu_tj" <tjlp at netease.com>;"vtkusers" <vtkusers at vtk.org>
主题:Re: [vtkusers] High memory cost of vtkDecimatePro for 3D model generation from DICOM series


On Fri, Mar 18, 2016 at 12:47 AM, Elvis Stansvik <elvis.stansvik at orexplore.com> wrote:

2016-03-18 3:19 GMT+01:00 David Gobbi <david.gobbi at gmail.com>:

You can segment an image with just one threshold (i.e. just the lower threshold).  It is not necessary to set a range.


Sorry for jumping in here, but I'm also pretty new to VTK, and what Liu describes sounds like something we will want to do soon: Allow the user to set a grayscale range, and only show the parts of the volume that falls within this range.


When you say "you can segment an image with just one threshold", do you mean that it somehow doesn't make sense to use two thresholds? If so, why? What if the use really wants to "extract" the parts of the volume where the scalar values are within some range?



It often makes sense to use a single threshold.  Examples:
1) segmenting bone from a CT image
2) removing background/noise from an MR image
3) segmenting vessels from a contrast image
Yes, there are also circumstances where two thresholds work better, but I've written more software that uses one threshold than that uses two.


The main point that I have been trying to make is that, if you want to get a smooth result out of vtkMarchingCubes, you should should give it a greyscale input, not a binary input.  In other words, you should not give marching cubes the output of vtkImageThreshold.


Marching cubes gives surfaces corresponding to isovalues.  If you have a range instead of a single threshold, then you should produce one surface for the lower end of the range, and another surface for the upper end of the range.  VTK surfaces are oriented, so you must reverse the sense of the upper-range surface (i.e. reverse the polygon winding and the normal directions).  Then you can combine the lower-range surface and the upper-range surface into a single polydata with vtkAppendPolyData.


If this sounds too complicated, then you can instead take the output from vtkImageThreshold, apply a mild gaussian blur to it, and apply marching cubes to the blurred data.  If you only have a binary mask (i.e. if you no longer have the original data) then this is a reasonable way to produce a greyscale input for marching cubes.  But if you have the original data, then a more accurate result can be achieved by feeding the original data into marching cubes, so that it uses the original greyscale values when it analyzes the voxels and produces the surface.


 - David
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