[Insight-users] Problem with Saving a segmented object

[Cameron Burnett]

I just tried a smaller DICOM data set, and it worked (well not the way I want it to, but it generated a vtk file). Is a 170MB DICOM data set normally too big to handle with region growing? Is it possible to perhaps buffer some to the file, clear the memory, then do the rest of it?? I'm not at all sure what I should do. I'd consider doing it slice by slice, but I read somewhere that all the 2D algorithms can be used for 3D as well. 



This is the output i'm getting. I was actually pleased that it did SOMETHING, but its obviously not what I want from my segmentation....

http://img371.imageshack.us/img371/6677/dicomtovtk1ju8.jpg

You can see the dicom object and the vtkPointWidget in the background. I'm using the point widget for the seed point, but for some reason it wants to colour all the way to the boundary of the widget. *shrug*. I'll just play around with the variables a bit I guess, unless anyone can recommend that I try anything else.

Thanks.



From: w_e_b_m_a_s_t_e_r_6_9 at hotmail.com
To: insight-users at itk.org
Date: Fri, 4 Apr 2008 01:11:15 +1000
Subject: [Insight-users] Problem with Saving a segmented object







Hi,

I've just implemented a mix of the DicomSeriesReadImageWrite2 and ConfidenceConnected algorithm examples for region growing segmentation. So basically, I want to segment a DICOM file and then save it as vtk or a similar file format (Unless there is a better way that anyone knows of).

The problem is that once I run the segmentation it takes 10 minutes in order to spit an error message back.

So what is it doing? Well, my program gets through to the execution of the writer pipeline quite quickly (writer->Update() ). After that the cpu is maxed out at 100% and my RAM is practically maxed out also (I have 2GB, and 360MB is taken up once I load my DICOM file onto the screen via the raycast method). Then after about 10 minutes I get an error in itkProcessObject.cxx. This is in the ProcessObject::UpdateOutputData function, where it calls  this->GenerateData(). When I mouse-over the exception in vc++ it says something about failing to allocate memory for the file.

I originally thought it had something to do with pixel type casting, because the pre-segmentation smoothing requires a float pixel type and I had just left it as float for the rest also. Then I tried casting it back to "signed short" before the segmentation stage.... but that did the same. 10 minutes is a long time to wait to see if a small change works.

So the main question is.... should it take 10 minutes for a 2GHz dual core cpu (with 2GB ram) to do region growing segmentation (then die, lol). Btw, the DICOM files are about 170MB for the whole 342 of them (about 500KB each file). 

Also, if anyone knows whats going on, or would like to request more information, then that would be great. I'm not expecting much though. 



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