[Insight-users] Fw: simple example of using any segmentation filter
Yinpeng Jin
yj76 at columbia . edu
Fri, 26 Jul 2002 10:31:30 -0400
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SimpleFuzzyConnectednessScalarImageFilter was designed to work on any =
dimension data. We have been using it
for both 2D and 3D, and it works fine as long as the right parameters =
are chosen.
The minimum set of parameters you need to run =
SimpleFuzzyConnectednessScalarImageFilter includes:
(1) a seed point that is inside the object of interest. =
SetObjectSeed();
(2) the estimation of the mean and variance of the object. SetMean, =
SetVariance.
(3) a threshold value to generate the binary segmented object. (between =
0 and 1). SetThreshold.
you don't need the exact value of mean/variance, but they should be =
close to the target object, otherwise you are expecting a black volume.
also, the threshold is very important.
There are some other parameters you could use to improve the =
segmentation and was also implemented in ITK, you need to read the =
reference of Fuzzy Connectedness segmentation which was listed inside =
the .h file.
bad choice of (2) (3) can easily cause an black volume image for the =
segmentation result.
you can use=20
filter->GetFuzzyScene();
to get a ITK::Image<ushort,3> object (in the case of 3D), which is the =
fuzzy scene. (the voxel value was scale to [0,65535]).
and then you can apply threshold using your own code or other ITK class. =
This avoids repeated computations if you got unsatifactory result just =
because the bad threshold value.
The running time varies a lot depending on how accurate is your =
estimation of the mean/variance, also the size of the volume and the =
size of the target object, and the noise level of the image data, etc...
it could take a very long time if you are dealling with high-res volume =
data. and infinite loops are unlikely to happen.
Yinpeng.
----- Original Message -----=20
From: Zein Salah=20
To: ITK Users=20
Sent: Friday, July 26, 2002 10:11 AM
Subject: [Insight-users] Fw: simple example of using any segmentation =
filter
Hi all,
=20
The SimpleFuzzyConnectednessScalarImageFilter works for a long time =
and produces just a black volume image, i.e. nothing at all can be seen.
has anybody an idea where is the problem
=20
thanks,
Zein
=20
----- Original Message -----=20
From: Zein Salah=20
To: ITK Users=20
Sent: Friday, July 26, 2002 2:48 PM
Subject: Fw: simple example of using any segmentation filter=20
=20
Hello ITK users,
=20
I have build a segmentation program that uses the=20
ConnectedThresholdImageFilter
on raw images that are read using MetaImageIO... and it worked.=20
=20
I tried to apply the same method with the=20
IsolatedConnectedImageFilter as well as with the =
SimpleFuzzyConnectednessScalarImageFilter
=20
the program went in an infinite loop.=20
=20
I realy do not know waht should the problem be.=20
1. Do not these filters work with volume data????
2. if they do, what are the parameters to be set?? to what values??
=20
=20
Thanks in advance for any kind of help.
=20
zein
=20
=20
=20
=
->8<------------->8<------------->8<------------->8<------------->8<-----=
-------->8<-
Zein I. Salah=20
Universit=E4t T=FCbingen, WSI-GRIS=20
Sand 14=20
72076 T=FCbingen=20
Email: salah@gris.uni-tuebingen.de / zeinsalah@hotmail.com
Tel.: (07071) 29 75465 (GRIS) , (07071) 96 44 39 (privat)=20
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<DIV><FONT face=3DArial size=3D2><FONT=20
face=3D"Times New Roman">SimpleFuzzyConnectednessScalarImageFilter was =
designed to=20
work on any dimension data. We have been using it</FONT></FONT></DIV>
<DIV><FONT size=3D2>for both 2D and 3D, and it works fine as long as the =
right=20
parameters are chosen.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>The minimum set of parameters you need =
to run <FONT=20
face=3D"Times New Roman">SimpleFuzzyConnectednessScalarImageFilter=20
includes:</FONT></FONT></DIV>
<DIV><FONT face=3DArial size=3D2>(1) a seed point that is inside the =
object of=20
interest. SetObjectSeed();</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>(2) the estimation of the mean and =
variance of the=20
object. SetMean, SetVariance.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>(3) a threshold value to generate the =
binary=20
segmented object. (between 0 and 1). SetThreshold.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>you don't need the exact value of =
mean/variance,=20
but they should be close to the target object, otherwise you are =
expecting a=20
black volume.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>also, the threshold is very =
important.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>There are some other parameters you =
could use to=20
improve the segmentation and was also implemented in ITK, you need to =
read the=20
reference of Fuzzy Connectedness segmentation which was listed inside =
the .h=20
file.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>bad choice of (2) (3) can easily cause =
an black=20
volume image for the segmentation result.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>you can use </FONT></DIV>
<DIV><FONT face=3DArial =
size=3D2>filter->GetFuzzyScene();</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>to get a ITK::Image<ushort,3> =
object (in the=20
case of 3D), which is the fuzzy scene. (the voxel value was scale to=20
[0,65535]).</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>and then you can apply threshold using =
your own=20
code or other ITK class. This avoids repeated computations if you got=20
unsatifactory result just because the bad threshold value.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>The running time varies a lot depending =
on how=20
accurate is your estimation of the mean/variance, also the size of the =
volume=20
and the size of the target object, and the noise level of the image =
data,=20
etc...</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>it could take a very long time if you =
are dealling=20
with high-res volume data. and infinite loops are unlikely to=20
happen.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=3DArial size=3D2>Yinpeng.</FONT></DIV>
<DIV> </DIV>
<DIV> </DIV>
<BLOCKQUOTE=20
style=3D"BORDER-LEFT: #000000 2px solid; MARGIN-LEFT: 5px; MARGIN-RIGHT: =
0px; PADDING-LEFT: 5px; PADDING-RIGHT: 0px">
<DIV style=3D"FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV=20
style=3D"BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: =
black"><B>From:</B>=20
<A href=3D"mailto:salah@gris.uni-tuebingen.de"=20
title=3Dsalah@gris.uni-tuebingen.de>Zein Salah</A> </DIV>
<DIV style=3D"FONT: 10pt arial"><B>To:</B> <A=20
href=3D"mailto:insight-users@public.kitware.com"=20
title=3Dinsight-users@public.kitware.com>ITK Users</A> </DIV>
<DIV style=3D"FONT: 10pt arial"><B>Sent:</B> Friday, July 26, 2002 =
10:11=20
AM</DIV>
<DIV style=3D"FONT: 10pt arial"><B>Subject:</B> [Insight-users] Fw: =
simple=20
example of using any segmentation filter</DIV>
<DIV><BR></DIV>
<DIV><FONT face=3DArial size=3D2>Hi all,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>The <FONT=20
face=3D"Times New Roman">SimpleFuzzyConnectednessScalarImageFilter =
works for a=20
long time and produces just a black volume image, i.e. nothing at all =
can be=20
seen.</FONT></FONT></DIV>
<DIV><FONT size=3D2>has anybody an idea where is the =
problem</FONT></DIV>
<DIV><FONT size=3D2></FONT> </DIV>
<DIV><FONT size=3D2>thanks,</FONT></DIV>
<DIV><FONT size=3D2>Zein</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV style=3D"FONT: 10pt arial">----- Original Message -----=20
<DIV style=3D"BACKGROUND: #e4e4e4; font-color: black"><B>From:</B> <A=20
href=3D"mailto:salah@gris.uni-tuebingen.de"=20
title=3Dsalah@gris.uni-tuebingen.de>Zein Salah</A> </DIV>
<DIV><B>To:</B> <A href=3D"mailto:insight-users@public.kitware.com"=20
title=3Dinsight-users@public.kitware.com>ITK Users</A> </DIV>
<DIV><B>Sent:</B> Friday, July 26, 2002 2:48 PM</DIV>
<DIV><B>Subject:</B> Fw: simple example of using any segmentation =
filter=20
</DIV></DIV>
<DIV><BR></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Hello ITK users,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I have build a segmentation =
program that=20
uses the </FONT></DIV>
<DIV><A class=3Del=20
=
href=3D"http://www.itk.org/Doxygen/html/classitk_1_1ConnectedThresholdIma=
geFilter.html">ConnectedThresholdImageFilter</A></DIV>
<DIV><FONT face=3DArial size=3D2>on raw images that are read using=20
MetaImageIO... and it worked. </FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I tried to apply the same method with =
the=20
</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>IsolatedConnectedImageFilter as well =
as with the=20
<FONT=20
face=3D"Times New =
Roman">SimpleFuzzyConnectednessScalarImageFilter</FONT></FONT></DIV>
<DIV><FONT size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>the program went in an infinite loop. =
</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I realy do not know waht should the =
problem be.=20
</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>1. Do not these filters work with =
volume=20
data????</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>2. if they do, what are the =
parameters to be=20
set?? to what values??</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Thanks in advance for any kind of=20
help.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>zein</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial=20
=
size=3D2>->8<------------->8<------------->8<----------=
--->8<------------->8<------------->8<-<BR>Zein=20
I. Salah <BR>Universit=E4t T=FCbingen, WSI-GRIS <BR>Sand 14 <BR>72076 =
T=FCbingen=20
<BR>Email: <A=20
=
href=3D"mailto:salah@gris.uni-tuebingen.de">salah@gris.uni-tuebingen.de</=
A> =20
/ <A =
href=3D"mailto:zeinsalah@hotmail.com">zeinsalah@hotmail.com</A><BR>Tel.: =
(07071) 29 75465 (GRIS) , (07071) 96 44 39 (privat)=20
</FONT></DIV></BLOCKQUOTE></BODY></HTML>
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