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Need advice on LV MRI segmentation
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Need advice on LV MRI segmentation
by Barry Branham
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Hi all,
I'm working on a project to segment left ventricular walls from 2D MRI images and would like to get advice on how to proceed with the epicardial walls. My project is to segment left ventricular walls (the round ones) from 2D MRI images. I'm using 2D because the main application uses Tagged MRI images for determining tissue displacements for input into an FEA application for determining wall stress/strains. And the Imaging sequence requires long patient breath holds so apparently they are limited in the number of slices output so my slice spacing is about 8mm. Fortunately they have recently also acquired non-tagged images that I can use for segmentation. I have had good luck segmenting the endocardial walls using IntensityWindow -> CurvatureFlow -> ConfidenceConnected, then DeformableMesh2DFilter which I converted from DeformableMesh3DFilter. The epicardial walls are harder because of the lack of large gradients on part of the outside (non-septal) wall. My current plan is to use a deformable model generated by getting the major axis from the endo wall and generating a slightly larger oriented ellipse from that. I need a good way to enlarge it to fit the epicardial wall. Thanks for any suggestions, Barry Branham Cardiothoracic Surgery Research Washington University School of Medicine St. Louis, MO _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Need advice on LV MRI segmentation
by Luis Ibanez
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Hi Barry,
Could you please post screenshots of your images to a public web site ? In particular, the original tagged MRI image, and the segmentation that you are obtaining so far. If we can see the images, it will be a lot easier to advise you on the potential segmentation methods that you may want to try. Regards, Luis -------------------- On Sun, Nov 8, 2009 at 9:36 PM, Barry Branham <bhb@...> wrote: > Hi all, > > I'm working on a project to segment left ventricular walls from 2D MRI > images and would like to get advice on how to proceed with the epicardial > walls. > > My project is to segment left ventricular walls (the round ones) from 2D MRI > images. I'm using 2D because the main application uses Tagged MRI images > for determining tissue displacements for input into an FEA application for > determining wall stress/strains. And the Imaging sequence requires long > patient breath holds so apparently they are limited in the number of slices > output so my slice spacing is about 8mm. Fortunately they have recently > also acquired non-tagged images that I can use for segmentation. I have had > good luck segmenting the endocardial walls using IntensityWindow -> > CurvatureFlow -> ConfidenceConnected, then > DeformableMesh2DFilter which I converted from DeformableMesh3DFilter. > > The epicardial walls are harder because of the lack of large gradients on > part of the outside (non-septal) wall. My current plan is to use a > deformable model generated by getting the major axis from the endo wall and > generating a slightly larger oriented ellipse from that. I need a good way > to enlarge it to fit the epicardial wall. > > Thanks for any suggestions, > Barry Branham > Cardiothoracic Surgery Research > Washington University School of Medicine > St. Louis, MO > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.html > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://www.itk.org/mailman/listinfo/insight-users > Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Need advice on LV MRI segmentation
by Barry Branham
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Hi Luis,
I just resurrected my website using Drupal this afternoon. It was either that or facebook. I put the Dicom file and two screen shots at http://branham.ws/?q=Navigation/4 I revisited BalloonForceFilter, Luis, and discovered you were actually right the first time in saying it was for 3D. It's just the description that is wrong. It is in fact BalloonForce3DFilter. The reason it was crashing for me was I was giving it a 2D Mesh and it was trying to access the 3rd dim components. The test app you mentioned "itk2DDeformableTest.cxx", uses Mesh<double> with the default Dimension parameter == 3 and then uses SphereMeshSource to initialize the mesh. So itk2DDeformableTest.cxx should be renamed and the description in itkBalloonForceFilter.h needs updating. Looking forward to any ideas on segmenting the Epi. Thanks, Barry Luis Ibanez wrote: > Hi Barry, > > Could you please post screenshots of your images to a public web site ? > > In particular, the original tagged MRI image, and the segmentation that > you are obtaining so far. > > If we can see the images, it will be a lot easier to advise you on the > potential segmentation methods that you may want to try. > > Regards, > > > Luis > > > -------------------- > On Sun, Nov 8, 2009 at 9:36 PM, Barry Branham <bhb@...> wrote: > >> Hi all, >> >> I'm working on a project to segment left ventricular walls from 2D MRI >> images and would like to get advice on how to proceed with the epicardial >> walls. >> >> My project is to segment left ventricular walls (the round ones) from 2D MRI >> images. I'm using 2D because the main application uses Tagged MRI images >> for determining tissue displacements for input into an FEA application for >> determining wall stress/strains. And the Imaging sequence requires long >> patient breath holds so apparently they are limited in the number of slices >> output so my slice spacing is about 8mm. Fortunately they have recently >> also acquired non-tagged images that I can use for segmentation. I have had >> good luck segmenting the endocardial walls using IntensityWindow -> >> CurvatureFlow -> ConfidenceConnected, then >> DeformableMesh2DFilter which I converted from DeformableMesh3DFilter. >> >> The epicardial walls are harder because of the lack of large gradients on >> part of the outside (non-septal) wall. My current plan is to use a >> deformable model generated by getting the major axis from the endo wall and >> generating a slightly larger oriented ellipse from that. I need a good way >> to enlarge it to fit the epicardial wall. >> >> Thanks for any suggestions, >> Barry Branham >> Cardiothoracic Surgery Research >> Washington University School of Medicine >> St. Louis, MO >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.html >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://www.itk.org/mailman/listinfo/insight-users >> >> > > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Need advice on LV MRI segmentation
by Luis Ibanez
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Hi Barry,
I couldn't access your web site today. Is it still available ? -- Also, we just committed a fix to the Doxygen documentation of the itkBalloonForceFilter: http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/Algorithms/itkBalloonForceFilter.h?root=Insight&r1=1.41&r2=1.42&sortby=date Thanks for helping us track this problem. Luis -------------------------------------------------------------- On Sun, Nov 15, 2009 at 10:19 PM, Barry Branham <bhb@...> wrote: > Hi Luis, > > I just resurrected my website using Drupal this afternoon. It was either > that or facebook. > I put the Dicom file and two screen shots at > http://branham.ws/?q=Navigation/4 > > I revisited BalloonForceFilter, Luis, and discovered you were actually right > the first time in saying it was for 3D. It's just the description that is > wrong. It is in fact BalloonForce3DFilter. The reason it was crashing for > me was I was giving it a 2D Mesh and it was trying to access the 3rd dim > components. The test app you mentioned "itk2DDeformableTest.cxx", uses > Mesh<double> with the default Dimension parameter == 3 and then uses > SphereMeshSource to initialize the mesh. So itk2DDeformableTest.cxx should > be renamed and the description in itkBalloonForceFilter.h needs updating. > > Looking forward to any ideas on segmenting the Epi. > > Thanks, > Barry > > > > Luis Ibanez wrote: >> >> Hi Barry, >> >> Could you please post screenshots of your images to a public web site ? >> >> In particular, the original tagged MRI image, and the segmentation that >> you are obtaining so far. >> >> If we can see the images, it will be a lot easier to advise you on the >> potential segmentation methods that you may want to try. >> >> Regards, >> >> >> Luis >> >> >> -------------------- >> On Sun, Nov 8, 2009 at 9:36 PM, Barry Branham <bhb@...> wrote: >> >>> >>> Hi all, >>> >>> I'm working on a project to segment left ventricular walls from 2D MRI >>> images and would like to get advice on how to proceed with the epicardial >>> walls. >>> >>> My project is to segment left ventricular walls (the round ones) from 2D >>> MRI >>> images. I'm using 2D because the main application uses Tagged MRI images >>> for determining tissue displacements for input into an FEA application >>> for >>> determining wall stress/strains. And the Imaging sequence requires long >>> patient breath holds so apparently they are limited in the number of >>> slices >>> output so my slice spacing is about 8mm. Fortunately they have recently >>> also acquired non-tagged images that I can use for segmentation. I have >>> had >>> good luck segmenting the endocardial walls using IntensityWindow -> >>> CurvatureFlow -> ConfidenceConnected, then >>> DeformableMesh2DFilter which I converted from DeformableMesh3DFilter. >>> >>> The epicardial walls are harder because of the lack of large gradients on >>> part of the outside (non-septal) wall. My current plan is to use a >>> deformable model generated by getting the major axis from the endo wall >>> and >>> generating a slightly larger oriented ellipse from that. I need a good >>> way >>> to enlarge it to fit the epicardial wall. >>> >>> Thanks for any suggestions, >>> Barry Branham >>> Cardiothoracic Surgery Research >>> Washington University School of Medicine >>> St. Louis, MO >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.html >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://www.itk.org/mailman/listinfo/insight-users >>> >>> >> >> > > Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Need advice on LV MRI segmentation
by Barry Branham
::
Rate this Message:
Hi Luis,
Thanks for pointing out my web site problem. It should be fixed now, let me know if it isn't. Luis Ibanez wrote: > Hi Barry, > > I couldn't access your web site today. > Is it still available ? > > -- > > Also, we just committed a fix to the Doxygen documentation of > the itkBalloonForceFilter: > http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/Algorithms/itkBalloonForceFilter.h?root=Insight&r1=1.41&r2=1.42&sortby=date > > > Thanks for helping us track this problem. > > > Luis > > > -------------------------------------------------------------- > On Sun, Nov 15, 2009 at 10:19 PM, Barry Branham <bhb@...> wrote: > >> Hi Luis, >> >> I just resurrected my website using Drupal this afternoon. It was either >> that or facebook. >> I put the Dicom file and two screen shots at >> http://branham.ws/?q=Navigation/4 >> >> I revisited BalloonForceFilter, Luis, and discovered you were actually right >> the first time in saying it was for 3D. It's just the description that is >> wrong. It is in fact BalloonForce3DFilter. The reason it was crashing for >> me was I was giving it a 2D Mesh and it was trying to access the 3rd dim >> components. The test app you mentioned "itk2DDeformableTest.cxx", uses >> Mesh<double> with the default Dimension parameter == 3 and then uses >> SphereMeshSource to initialize the mesh. So itk2DDeformableTest.cxx should >> be renamed and the description in itkBalloonForceFilter.h needs updating. >> >> Looking forward to any ideas on segmenting the Epi. >> >> Thanks, >> Barry >> >> >> >> Luis Ibanez wrote: >> >>> Hi Barry, >>> >>> Could you please post screenshots of your images to a public web site ? >>> >>> In particular, the original tagged MRI image, and the segmentation that >>> you are obtaining so far. >>> >>> If we can see the images, it will be a lot easier to advise you on the >>> potential segmentation methods that you may want to try. >>> >>> Regards, >>> >>> >>> Luis >>> >>> >>> -------------------- >>> On Sun, Nov 8, 2009 at 9:36 PM, Barry Branham <bhb@...> wrote: >>> >>> >>>> Hi all, >>>> >>>> I'm working on a project to segment left ventricular walls from 2D MRI >>>> images and would like to get advice on how to proceed with the epicardial >>>> walls. >>>> >>>> My project is to segment left ventricular walls (the round ones) from 2D >>>> MRI >>>> images. I'm using 2D because the main application uses Tagged MRI images >>>> for determining tissue displacements for input into an FEA application >>>> for >>>> determining wall stress/strains. And the Imaging sequence requires long >>>> patient breath holds so apparently they are limited in the number of >>>> slices >>>> output so my slice spacing is about 8mm. Fortunately they have recently >>>> also acquired non-tagged images that I can use for segmentation. I have >>>> had >>>> good luck segmenting the endocardial walls using IntensityWindow -> >>>> CurvatureFlow -> ConfidenceConnected, then >>>> DeformableMesh2DFilter which I converted from DeformableMesh3DFilter. >>>> >>>> The epicardial walls are harder because of the lack of large gradients on >>>> part of the outside (non-septal) wall. My current plan is to use a >>>> deformable model generated by getting the major axis from the endo wall >>>> and >>>> generating a slightly larger oriented ellipse from that. I need a good >>>> way >>>> to enlarge it to fit the epicardial wall. >>>> >>>> Thanks for any suggestions, >>>> Barry Branham >>>> Cardiothoracic Surgery Research >>>> Washington University School of Medicine >>>> St. Louis, MO >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.html >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://www.itk.org/mailman/listinfo/insight-users >>>> >>>> >>>> >>> >> > > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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