[Insight-users] Problem with Saving a segmented object

[Luis Ibanez]

Hi Cameron,

It shouldn't be a problem to handle a 170Mb image, either for
reading, writing, and running a region growing segmentation.

  ...You may have additional filters in the pipeline....

Could you please describe the full pipeline ?

and also provide the information of your image:

   a) number of pixels
   b) Image Modality / pixel type


Thanks


     Luis


-------------------------
Cameron Burnett wrote:
> 
> 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.
> 
> 
> 
>     ------------------------------------------------------------------------
>     Find out: SEEK Salary Centre Are you paid what you're worth?
>     <http://a.ninemsn.com.au/b.aspx?URL=http://ninemsn.seek.com.au/career-resources/salary-centre/?tracking%3Dsk:het:sc:nine:0:hot:text&_t=764565661&_r=OCT07_endtext_salary&_m=EXT>
> 
> 
> 
> ------------------------------------------------------------------------
> Grab it. You dream job is up for grabs. 
> <http://mycareer.com.au/?s_cid=596065 >
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users