[Insight-users] Fuzzy connectedness 3D
Alex Houston
ahouston_29@yahoo.com
Wed May 19 19:14:02 EDT 2004
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Hi luis,
I didn't have any problem reading the dicom series CT images. I used part of code from DicomSeriesReadImageWrite.cxx and checked output as .img file.
I have CT series of chest region and trying to segment the heart region.
I did compile in debug mode ( as I need to track some parts of code). I did that in release mode too but timming didn't improve.
About providing the mean/variance I used confidenceConnectedFilter, I have also tried hardcoding the values of mean/variance but the time to run remained the same.
I saw one demo which has input as RAW files, I am have whole directory with dicom images. It doesn't accept the directory as input.
Thanks for your help
A. Houston
Luis Ibanez <luis.ibanez@kitware.com> wrote:
Hi Alex,
There shouldn't be any problem for reading your
data set from a group of DICOM slices and passing
it to the FuzzyConnectedness filter.
The 2 hours that you are experiencing for a
512 x 512 x 70 is excesive.
Using this filter for extracting the ventricles
from one of the BrainWeb images (181 x 200 x 180 )
takes about 1 minute in a Pentium 4, at 2.4Ghz.
What anatomical structure are you trying to
segment from your CT data ?
Some questions:
1) Did you compile your code for Release ?
(e.g. -O3 in gcc, or /Release in VisualStudio).
2) How are you providing the estimation of the
Mean value to the filter ?
3) How are you providing the estimation of the
Variance to the filter ?
You may want to experiment first with the demo
application
InsightApplications/
RegionGrowingSegmentaiton
where the FuzzyConnectendes filter is on the GUI.
Note that you must provide Variance, not standard
deviation. Therefore typical values for an MRI are
in the range of 100s while values in a CT may be
in the range of 1e4 to 1e6.
Regards,
Luis
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<DIV>
<DIV>Hi luis,</DIV>
<DIV> </DIV>
<DIV>I didn't have any problem reading the dicom series CT images. I used part of code from DicomSeriesReadImageWrite.cxx and checked output as .img file. </DIV>
<DIV> </DIV>
<DIV>I have CT series of chest region and trying to segment the heart region.</DIV>
<DIV> </DIV>
<DIV>I did compile in debug mode ( as I need to track some parts of code). I did that in release mode too but timming didn't improve.</DIV>
<DIV> </DIV>
<DIV>About providing the mean/variance I used <FONT size=2>confidenceConnectedFilter, I have also tried hardcoding the values of mean/variance but the time to run remained the same.</FONT></DIV>
<DIV> </DIV>
<DIV>I saw one demo which has input as RAW files, I am have whole directory with dicom images. It doesn't accept the directory as input.</DIV>
<DIV> </DIV>
<DIV>Thanks for your help</DIV>
<DIV> </DIV>
<DIV>A. Houston</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV><BR><BR><B><I>Luis Ibanez <luis.ibanez@kitware.com></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"><BR>Hi Alex,<BR><BR>There shouldn't be any problem for reading your<BR>data set from a group of DICOM slices and passing<BR>it to the FuzzyConnectedness filter.<BR><BR>The 2 hours that you are experiencing for a<BR>512 x 512 x 70 is excesive.<BR><BR>Using this filter for extracting the ventricles<BR>from one of the BrainWeb images (181 x 200 x 180 )<BR>takes about 1 minute in a Pentium 4, at 2.4Ghz.<BR><BR>What anatomical structure are you trying to<BR>segment from your CT data ?<BR><BR><BR>Some questions:<BR><BR>1) Did you compile your code for Release ?<BR>(e.g. -O3 in gcc, or /Release in VisualStudio).<BR><BR>2) How are you providing the estimation of the<BR>Mean value to the filter ?<BR><BR>3) How are you providing the estimation of the<BR>Variance to the filter ?<BR><BR><BR><BR>You may want to experiment first with the
demo<BR>application<BR><BR>InsightApplications/<BR>RegionGrowingSegmentaiton<BR><BR><BR>where the FuzzyConnectendes filter is on the GUI.<BR>Note that you must provide Variance, not standard<BR>deviation. Therefore typical values for an MRI are<BR>in the range of 100s while values in a CT may be<BR>in the range of 1e4 to 1e6.<BR><BR><BR>Regards,<BR><BR><BR>Luis<BR><BR><BR></BLOCKQUOTE></DIV><p>
<hr size=1><font face=arial size=-1>Do you Yahoo!?<br><a href="http://pa.yahoo.com/*http://us.rd.yahoo.com/evt=24311/*http://promo.yahoo.com/sbc/">SBC Yahoo!</a> - Internet access at a great low price.
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