[Insight-users] problem with CellularSegmentation
Luis Ibanez
luis.ibanez at kitware.com
Thu Jan 26 20:19:52 EST 2006
Hi Pavel,
Could you please try "SNAP" ?
This application can be found in
InsightApplications/SNAP
SNAP is another applications that combines
ITK, VTK and FLTK.
It may help us to figure out what is wrong
with your current configuration.
Please let us know what you find.
Thanks
Luis
---------------------
Pavel Tomancak wrote:
> Louis,
>
> I am on Mac OS X 10.3.4. The itkReadITKImageShowVTK runs fine. It opens
> the image in a Carbon window.
>
> CellularSegmentation needs X11, at least in my current set-up.
>
> I re-installed VTK from scratch and pointed it to tiff, jpeg and png
> libs installed by fink under /sw/lib
>
> No difference.
>
> Any ideas ?
>
> PAvel
>
>> Yeap, this may be related to your installation of VTK.
>>
>>
>>
>> The CellularSegmentation application uses VTK while the
>> Morphogenesis application uses OpenGL, that was in fact
>> one of the improvements in the CellularSegmentation app.
>>
>> Do you manage to run any other VTK applications in your
>> machine ?
>>
>> What is your platform ?
>>
>> You could try the example
>>
>>
>> InsightApplications/
>> Auxiliary/
>> vtk/
>> itkReadITKImageShowVTK.cxx
>>
>>
>> This is the minimal application that loads an image
>> using ITK and display that image using VTK.
>>
>>
>>
>> Please let us know what you find.
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>>
>> --------------------
>> Pavel Tomancak wrote:
>>
>>> Hi Luis,
>>> Still struggling.
>>>
>>>> Here is the simplest demo of the CellularSegmentation application.
>>>>
>>>>
>>>> 1) run the application
>>>
>>> ok
>>>
>>>> 2) Click on the "Load Image" button
>>>
>>> ok
>>>
>>>> 3) Select the image: Insight/Examples/Data/BrainProtonDensitySlice.png
>>>> (the image should appear on the window).
>>>
>>> Unfortunately I see no image. There is no error message.
>>> Just a simple question, could this have anything to do with my
>>> installation of VTK ? The Morphogenesis program is able to load the
>>> image and it does not depend on VTK. Just guessing.
>>> Thanks for your help.
>>> PAvel
>>>
>>>> 4) Click with the mouse on the ventricles (the bright areas close to
>>>> the center of the brain). A green circle should be left at the
>>>> point where you clicked.
>>>>
>>>> 5) Click on the "Play" button.
>>>>
>>>> 6) At this point the bacteria will start reproducing on the image,
>>>> and in a matter of seconds they should have filled the ventricles.
>>>>
>>>> 7) You can get a view of the cells connections by selecting
>>>> "Display: Real Neighbors" instead of the default "Cell Walls.
>>>>
>>>> 8) At any point you can pause the cells and change the Low and High
>>>> threshold values.
>>>>
>>>> 9) You can restart the colony by clicking on the "X" button.
>>>>
>>>>
>>>>
>>>> Please let us know if you find any problem running this minimal demo.
>>>>
>>>>
>>>>
>>>> Your idea of creating niches with different populations of cells
>>>> is great. A similar concept is used in level sets and it is commonly
>>>> termed as multi-phase level sets. This behavior will be very natural
>>>> on Cellular Algorithms. It will be great if we implement this as a
>>>> gene network first, so then you can simply load pre-engineered genomes
>>>> on the cells and don't have to do any further code modifications on
>>>> them. Down the line we could have Evolutionary Algorithms that train
>>>> those pre-engineered genomes, just as Biologists are doing today with
>>>> Directed-Evolution.
>>>>
>>>>
>>>> Short range cell-cell communication is already possible, by using the
>>>> neighbor coonections that you will see when you run the application.
>>>>
>>>>
>>>> We will be happy to give you some hints on how to implement your idea
>>>> of multiple cellular populations. Just let us know.
>>>>
>>>>
>>>>
>>>> BTW, Note that these algorithms extend naturally to N-Dimensions.
>>>> We just need to modify the template argument of the cells.
>>>> The main changes will be on the visualization and the GUI.
>>>>
>>>>
>>>>
>>>> Regards,
>>>>
>>>>
>>>>
>>>> Luis
>>>>
>>>>
>>>>
>>>> ---------------------
>>>> Pavel Tomancak wrote:
>>>>
>>>>> Hi Luis,
>>>>> Thanks again for the useful pointers. I installed VTK as best I
>>>>> could and the CellularSegmentation tool, but I cannot load any
>>>>> images. The window is responsive, but no matter what I load
>>>>> (jpeg, tiff) nothing shows up. I have no error message to
>>>>> substantiate this claim.
>>>>> I would say there are several well understood cell behaviours
>>>>> that could be implemented, for example establishment of
>>>>> compartment boundary, where two populations of cells do not mix
>>>>> according to expression of certain key genes. That could
>>>>> facilitate segmentation of images by defining two colonies, one
>>>>> that grows on background and one everywhere else. It would
>>>>> require short range cell-cell communication between neighboring
>>>>> cell.
>>>>> Well at this point I just want to get the CellularSegmentation
>>>>> running. Small step for humankind but a big step for me. :-)
>>>>> Sorry for bothering you with this.
>>>>> Best
>>>>> PAvel
>>>>> --------------------------------------------------------------------
>>>>> -- -- -----------
>>>>> Pavel Tomancak, Ph.D.
>>>>> Group Leader
>>>>> Max Planck Institute of Molecular Cell Biology and Genetics
>>>>> Pfotenhauerstr. 108
>>>>> D-01307 Dresden Tel.: +49 351 210 2670
>>>>> Germany Fax: +49 351 210 2020
>>>>> tomancak at mpi-cbg.de
>>>>> http://www.mpi-cbg.de
>>>>> --------------------------------------------------------------------
>>>>> -- -- -----------
>>>>> On Jan 25, 2006, at 3:42 PM, Luis Ibanez wrote:
>>>>>
>>>>>>
>>>>>> Hi Pavel,
>>>>>>
>>>>>> The Species that was better debugged is the "Gradient Eating
>>>>>> Bacteria",
>>>>>> altough the actual code was not quite finished, so it is not really
>>>>>> using the Gradient of the image yet. :-(
>>>>>>
>>>>>> In practice, this bacteria is using only a intensity range. The
>>>>>> lower
>>>>>> and upper values of that intensity range are written in the .dat
>>>>>> file
>>>>>> (which is a very primitive mechanism for passing data... I have to
>>>>>> admit). The x,y coordinate of the pixel where the egg is placed are
>>>>>> also provided in that .dat file.
>>>>>>
>>>>>> You should really give a try to the CelluarSegmentation tool,
>>>>>> because
>>>>>> we wrote it after struggling the the Morphogenesis application.
>>>>>> In the
>>>>>> CelluarSegmentation app, there is a single bacteria, and it is
>>>>>> following
>>>>>> the same rules as the (so-called) "Gradient Eating Bacteria" in the
>>>>>> Morphogenesis example. However that user interaction is much
>>>>>> better in
>>>>>> the CellularSegmentation app, because you can:
>>>>>>
>>>>>> 1) Place the egg in the image by simply clicking on the image
>>>>>> with the mouse,
>>>>>>
>>>>>> 2) You can also change the lower and upper values of the intensity
>>>>>> range for which the bacteria is allowed to replicate.
>>>>>>
>>>>>> 3) You can select the visualization to show the mesh connections,
>>>>>> or just the cells, or the bounding polygon. (this last option is
>>>>>> not that useful).
>>>>>>
>>>>>> 4) You can reset the colony, and go back to the one-egg state,
>>>>>> and restart the replication process.
>>>>>>
>>>>>>
>>>>>>
>>>>>> The Cellular Segmentation paradigm is intended to provide a
>>>>>> framework
>>>>>> where you could program the genome of different cells in order to
>>>>>> obtain particular behaviors. For example, the gradient eating
>>>>>> bacteria
>>>>>> was intended to migrate through the image, by moving in the
>>>>>> direction
>>>>>> of the image gradient. In this way, it was intended to behave as a
>>>>>> contour detection organism.
>>>>>>
>>>>>>
>>>>>> The long-term goal of the Morphogenesis example was to get to cells
>>>>>> with more complex genomes that will allow for differentiation and
>>>>>> therefore will be capable of creating realisting multi-cellular
>>>>>> organisms, instead of just bacterial colonies. Those organisms
>>>>>> could
>>>>>> have more complex behaviors since they could have specialized cells
>>>>>> to be sensors, other to be locomotion elements and so on. The idea
>>>>>> was to get to customized organisms, that were programmed to perform
>>>>>> image processing tasks such as detection, pattern recognition, model
>>>>>> to image registration, and so on.
>>>>>>
>>>>>>
>>>>>> You probably will be intereseted in the "Deformable Organisms" work
>>>>>> performed by the team of Dr. Ghassan Hamarneh at Simon Fraser
>>>>>> University. This work was presented at MICCAI in 2001 and recently
>>>>>> published too in Medical Image Analysis journal.
>>>>>>
>>>>>> http://www.cs.sfu.ca/~hamarneh/
>>>>>>
>>>>>>
>>>>>> The point of view of Biologist will be extremly helpful for further
>>>>>> developing the paradigm of Cell-based image processing. So we will
>>>>>> have more that happy to hear from you any suggestions that can
>>>>>> help improved this framework.
>>>>>>
>>>>>>
>>>>>>
>>>>>> Engineering the genome of real bacteria (E. Coli) has been done
>>>>>> recently with the purpose of performing image processing.Mechanisms
>>>>>> such as edge detection are easily implemented by interaction of a
>>>>>> couple of genes, just in the same way the the cones in the retina
>>>>>> detect edges. (This was published in Nature recently):
>>>>>>
>>>>>> "Synthetic biology: engineering Escherichia coli to see light."
>>>>>> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
>>>>>> cmd=Retrieve&db=PubMed&list_uids=16306980&dopt=Citation
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> You are probably aware of the following works, but.. in any case
>>>>>> they are quite interesting reading if you are motivated to look
>>>>>> further on the notions of Computational power of Cellular Automata,
>>>>>> and the interrelationships between biology and computer science:
>>>>>>
>>>>>>
>>>>>>
>>>>>> John Von Neumann, "Self-Replicating Automata"
>>>>>> http://en.wikipedia.org/wiki/John_von_Neumann
>>>>>> http://en.wikipedia.org/wiki/Self-replication
>>>>>>
>>>>>>
>>>>>> Alan Turing, "The Chemical Basis of Morphogenesis" 1952.
>>>>>> http://en.wikipedia.org/wiki/Alan_Turing
>>>>>>
>>>>>>
>>>>>>
>>>>>> Stephen Wolfram, "A New Kind of Science"
>>>>>> http://www.wolframscience.com/thebook.html
>>>>>>
>>>>>>
>>>>>>
>>>>>> Azriel Rosenfeld, "Picture Languages"
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>>
>>>>>>
>>>>>> Luis
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> -----------------------
>>>>>> Pavel Tomancak wrote:
>>>>>>
>>>>>>> Hi Luis,
>>>>>>> Thanks for the quick response. Yes, it works now. I am still
>>>>>>> having troubles growing the colonies on top of an image, but
>>>>>>> I haven't played around with it the .dat files yet.
>>>>>>> I will look at the other applications that you mentioned. The
>>>>>>> morphogenesis approximation of cellular automata is
>>>>>>> particularly appealing to biologist, since it is so
>>>>>>> intuitive. I think this approach has great potential.
>>>>>>> I am quite sure I will be back to you or the mailing lists with
>>>>>>> more questions soon.
>>>>>>> All The Best
>>>>>>> PAvel
>>>>>>> ------------------------------------------------------------------
>>>>>>> -- -- -- -----------
>>>>>>> Pavel Tomancak, Ph.D.
>>>>>>> Group Leader
>>>>>>> Max Planck Institute of Molecular Cell Biology and Genetics
>>>>>>> Pfotenhauerstr. 108
>>>>>>> D-01307 Dresden Tel.: +49 351 210 2670
>>>>>>> Germany Fax: +49 351 210 2020
>>>>>>> tomancak at mpi-cbg.de
>>>>>>> http://www.mpi-cbg.de
>>>>>>> ------------------------------------------------------------------
>>>>>>> -- -- -- -----------
>>>>>>> On Jan 24, 2006, at 11:05 PM, Luis Ibanez wrote:
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi Pavel
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks for pointing this out.
>>>>>>>>
>>>>>>>>
>>>>>>>> You just found a bug !
>>>>>>>>
>>>>>>>>
>>>>>>>> This bug seems to have been introduced recently when we replaced
>>>>>>>> the use of clock() functions with calls to the itk::RealTimeClock.
>>>>>>>>
>>>>>>>>
>>>>>>>> The bug is that we use a SmartPointer to a RealTimeClock but never
>>>>>>>> create it by invoking the New() operator.
>>>>>>>>
>>>>>>>> This has now been fixed in the CVS repository:
>>>>>>>>
>>>>>>>> http://www.itk.org/cgi-bin/viewcvs.cgi/Morphogenesis/
>>>>>>>> CellsViewerBase.cxx?
>>>>>>>> root=InsightApplications&sortby=date&r2=1.28&r1=1.27
>>>>>>>>
>>>>>>>> In order to fix it in your local copy, you can update your CVS
>>>>>>>> checkout, or you could simply add the following line to the
>>>>>>>> constructor of the CellsViewerBase class in the file
>>>>>>>>
>>>>>>>>
>>>>>>>> InsightApplications/
>>>>>>>> Morphogenesis/
>>>>>>>> CellsViewerBase.cxx
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Note that this is not the traditional approach of Cellular
>>>>>>>> Automata
>>>>>>>> that is implemented using the pixels of an image as the automata.
>>>>>>>> In this case we use the nodes of an itk::Mesh as the automata.
>>>>>>>> In this
>>>>>>>> way we can easily insert and remove nodes (cells) from that mesh.
>>>>>>>>
>>>>>>>>
>>>>>>>> One direction that we were anticipating to explore was to actually
>>>>>>>> program the cells using a synthetic Gene Network, such as the one
>>>>>>>> proposed by Platzer at the German Cancer Research Center (DKFZ)
>>>>>>>>
>>>>>>>>
>>>>>>>> http://mbi.dkfz-heidelberg.de/projects/cellsim/
>>>>>>>>
>>>>>>>>
>>>>>>>> In that way, the State Machine controlling the behavior of the
>>>>>>>> cell
>>>>>>>> will be defined by the interactions between the Genes and their
>>>>>>>> protein products.
>>>>>>>>
>>>>>>>> So far the State Machine of each one of the automata is pretty
>>>>>>>> much
>>>>>>>> hard coded according to the species that you select.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> If you are interested in this area, you may want to try also the
>>>>>>>> CellularSegmentation example that is available in the directory:
>>>>>>>>
>>>>>>>>
>>>>>>>> InsightApplications/
>>>>>>>> CellularSegmentation/
>>>>>>>>
>>>>>>>>
>>>>>>>> This is a more recent example application than "Morphogenesis".
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Other applications of traditional Cellular Automata approaches can
>>>>>>>> be used in the Voting filters and the Hole Filling filters. You
>>>>>>>> will find descriptions of these filter in the ITK Software Guide
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> http://www.itk.org/ItkSoftwareGuide.pdf
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Please let us know if you find any problems.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Luis
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --------------------
>>>>>>>> Pavel Tomancak wrote:
>>>>>>>>
>>>>>>>>> My experience with C++ is very limited, so some of this may
>>>>>>>>> sound a bit naive. I am a biologist after all.
>>>>>>>>> I downloaded InsightToolkit-2.4.0 and compiled it into /
>>>>>>>>> Applications/itk_binary on Mac OS X 10.3.9 with Xcode 1.5
>>>>>>>>> and upgraded gcc to 3.3. I used the default cmake options,
>>>>>>>>> no Examples, no Tests.
>>>>>>>>> Everything seems fine after make, which I suspect means
>>>>>>>>> nothing. Hello World works.
>>>>>>>>> Now, I downloaded the InsightApplications-2.4.0, meddled
>>>>>>>>> slightly with CMakeLists.txt to skip to the Morphogenesis
>>>>>>>>> part. (I comment every SUBDIR before Morphogenesis,
>>>>>>>>> otherwise it takes too long to get there, couldn't figure
>>>>>>>>> any other way).
>>>>>>>>> I installed fltk-1.1.7 and pointed cmake to it, I also change
>>>>>>>>> the USE_FLTK to ON.
>>>>>>>>> Now I run make in the dir where I unpackaged the
>>>>>>>>> InsightApplication,
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 2> again everything seems fine, voila - a Morphogenesis
>>>>>>>> application appears.
>>>>>>>>
>>>>>>>>> It starts, windows appear, images can be loaded, zoomed and
>>>>>>>>> so on. I can create any species egg I want, but, now it
>>>>>>>>> comes, after clicking on play it invariantly crashes.
>>>>>>>>> Below please find the error messages which are truly
>>>>>>>>> incomprehensible to me. They are not always the same, but
>>>>>>>>> often there is a line like this
>>>>>>>>> 0 libITKCommon.dylib 0x013a1228
>>>>>>>>> itk::RealTimeClock::GetTimeStamp() const + 0x78
>>>>>>>>> I would appreciate any help, this whole application of
>>>>>>>>> cellular automata to image processing is totally
>>>>>>>>> fascinating. I am very eager to try it on my images.
>>>>>>>>> Thanks in advance
>>>>>>>>> PAvel
>>>>>>>>> Here comes the error message
>>>>>>>>> Date/Time: 2006-01-24 17:57:06 +0100
>>>>>>>>> OS Version: 10.3.9 (Build 7W98)
>>>>>>>>> Report Version: 2
>>>>>>>>> Command: Morphogenesis
>>>>>>>>> Path: /Users/tomancak/Desktop/InsightApplications-2.4.0/
>>>>>>>>> Morphogenesis/ Morphogenesis
>>>>>>>>> Version: ??? (???)
>>>>>>>>> PID: 10843
>>>>>>>>> Thread: 0
>>>>>>>>> Exception: EXC_BAD_ACCESS (0x0001)
>>>>>>>>> Codes: KERN_PROTECTION_FAILURE (0x0002) at 0x00000048
>>>>>>>>> Thread 0 Crashed:
>>>>>>>>> 0 libITKCommon.dylib 0x013a1228
>>>>>>>>> itk::RealTimeClock::GetTimeStamp() const + 0x78
>>>>>>>>> 1 Morphogenesis 0x00007eb8
>>>>>>>>> bio::CellsViewerBase::GetElapsedTime() const + 0x34
>>>>>>>>> 2 Morphogenesis 0x00009708
>>>>>>>>> bio::CellsViewerCommand::Execute(itk::Object const*,
>>>>>>>>> itk::EventObject const&) + 0xd4
>>>>>>>>> 3 Morphogenesis 0x00009828
>>>>>>>>> bio::CellsViewerCommand::Execute(itk::Object*,
>>>>>>>>> itk::EventObject const&) + 0x50
>>>>>>>>> 4 libITKCommon.dylib 0x01396f74
>>>>>>>>> itk::SubjectImplementation::InvokeEvent(itk::EventObject
>>>>>>>>> const&, itk::Object*) + 0xe8
>>>>>>>>> 5 libITKCommon.dylib 0x0139802c
>>>>>>>>> itk::Object::InvokeEvent(itk::EventObject const&) + 0x40
>>>>>>>>> 6 Morphogenesis 0x0000b47c
>>>>>>>>> bio::CellularAggregate::AdvanceTimeStep() + 0x1cc
>>>>>>>>> 7 Morphogenesis 0x0000782c
>>>>>>>>> bio::CellsViewerBase::Run() + 0xbc
>>>>>>>>> 8 Morphogenesis 0x00009204
>>>>>>>>> bio::CellsViewer::Run() + 0x20
>>>>>>>>> 9 Morphogenesis 0x00010a00
>>>>>>>>> CellsViewerGUI::cb_3_i(Fl_Button*, void*) + 0x40
>>>>>>>>> 10 Morphogenesis 0x00010a58
>>>>>>>>> CellsViewerGUI::cb_3(Fl_Button*, void*) + 0x44
>>>>>>>>> 11 Morphogenesis 0x0004061c
>>>>>>>>> Fl_Button::handle (int) + 0x3cc
>>>>>>>>> 12 Morphogenesis 0x00021998 send(int,
>>>>>>>>> Fl_Widget*, Fl_Window*) + 0xc0
>>>>>>>>> 13 Morphogenesis 0x00021cf4
>>>>>>>>> Fl::handle(int, Fl_Window*) + 0x33c
>>>>>>>>> 14 Morphogenesis 0x00024268
>>>>>>>>> carbonMouseHandler(OpaqueEventHandlerCallRef*,
>>>>>>>>> OpaqueEventRef*, void*) + 0x2dc
>>>>>>>>> 15 <<00000000>> 0x92882e50 0 + 0x92882e50
>>>>>>>>> 16 <<00000000>> 0x928830c4 0 + 0x928830c4
>>>>>>>>> 17 <<00000000>> 0x92895530 0 + 0x92895530
>>>>>>>>> 18 Morphogenesis 0x0002342c
>>>>>>>>> carbonDispatchHandler(OpaqueEventHandlerCallRef*,
>>>>>>>>> OpaqueEventRef*, void*) + 0xf0
>>>>>>>>> 19 <<00000000>> 0x92882e50 0 + 0x92882e50
>>>>>>>>> 20 <<00000000>> 0x928830c4 0 + 0x928830c4
>>>>>>>>> 21 <<00000000>> 0x92895530 0 + 0x92895530
>>>>>>>>> 22 Morphogenesis 0x000238a4
>>>>>>>>> do_queued_events (double) + 0x178
>>>>>>>>> 23 Morphogenesis 0x00023998
>>>>>>>>> fl_wait(double) + 0x1c
>>>>>>>>> 24 Morphogenesis 0x00020f1c
>>>>>>>>> Fl::wait(double) + 0x84
>>>>>>>>> 25 Morphogenesis 0x00020f8c Fl::run() +
>>>>>>>>> 0x38
>>>>>>>>> 26 Morphogenesis 0x0000facc main + 0x34c
>>>>>>>>> 27 Morphogenesis 0x00003204 _start +
>>>>>>>>> 0x188 (crt.c:267)
>>>>>>>>> 28 dyld 0x8fe1a278 _dyld_start
>>>>>>>>> + 0x64
>>>>>>>>> Thread 1:
>>>>>>>>> 0 libSystem.B.dylib 0x900078b8
>>>>>>>>> mach_msg_trap + 0x8
>>>>>>>>> 1 libSystem.B.dylib 0x90007438 mach_msg + 0x38
>>>>>>>>> 2 com.unsanity.ape 0xc0002c14
>>>>>>>>> __ape_internal + 0xce4
>>>>>>>>> 3 com.unsanity.ape 0xc0001a28 __ape_agent
>>>>>>>>> + 0x40
>>>>>>>>> 4 libSystem.B.dylib 0x90024990
>>>>>>>>> _pthread_body + 0x28
>>>>>>>>> Thread 2:
>>>>>>>>> 0 libSystem.B.dylib 0x900078b8
>>>>>>>>> mach_msg_trap + 0x8
>>>>>>>>> 1 libSystem.B.dylib 0x90007438 mach_msg + 0x38
>>>>>>>>> 2 ...lagutin.audio_hijack.server 0x01194e60 ah_serv_loop
>>>>>>>>> + 0x58
>>>>>>>>> 3 libSystem.B.dylib 0x90024990
>>>>>>>>> _pthread_body + 0x28
>>>>>>>>> PPC Thread State:
>>>>>>>>> srr0: 0x013a1228 srr1: 0x0200f030 vrsave:
>>>>>>>>> 0x00000000
>>>>>>>>> cr: 0x82822222 xer: 0x20000004 lr: 0x013a11dc ctr:
>>>>>>>>> 0x90008b60
>>>>>>>>> r0: 0x800eeea0 r1: 0xbffff040 r2: 0x00000000 r3:
>>>>>>>>> 0x00000000
>>>>>>>>> r4: 0x00000000 r5: 0x00000000 r6: 0x0006b2df r7:
>>>>>>>>> 0x43d65c61
>>>>>>>>> r8: 0x000eeea0 r9: 0x015311c8 r10: 0x43300000 r11:
>>>>>>>>> 0x007b77ee
>>>>>>>>> r12: 0x000f4240 r13: 0x00000000 r14: 0x00000000 r15:
>>>>>>>>> 0x00000000
>>>>>>>>> r16: 0x00000000 r17: 0x00000000 r18: 0x00000000 r19:
>>>>>>>>> 0x00000000
>>>>>>>>> r20: 0x00000002 r21: 0x00000000 r22: 0x0396b290 r23:
>>>>>>>>> 0x03929a00
>>>>>>>>> r24: 0xbffff7c0 r25: 0x00000030 r26: 0x0000002f r27:
>>>>>>>>> 0x00128a3c
>>>>>>>>> r28: 0x00128a40 r29: 0xbffff310 r30: 0xbffff040 r31:
>>>>>>>>> 0x013a11c8
>>>>>>>>> Binary Images Description:
>>>>>>>>> 0x1000 - 0x126fff Morphogenesis
>>>>>>>>> /Users/tomancak/Desktop/
>>>>>>>>> InsightApplications-2.4.0/Morphogenesis/ Morphogenesis
>>>>>>>>> 0x24c000 - 0x24dfff libITKznz.dylib /Applications/
>>>>>>>>> itk_binary/bin/libITKznz.dylib
>>>>>>>>> 0x267000 - 0x282fff libITKniftiio.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libITKniftiio.dylib
>>>>>>>>> 0x298000 - 0x2c8fff libITKNrrdIO.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libITKNrrdIO.dylib
>>>>>>>>> 0x2e8000 - 0x2fafff libitkzlib.dylib /Applications/
>>>>>>>>> itk_binary/bin/libitkzlib.dylib
>>>>>>>>> 0x405000 - 0x43bfff libitkjpeg12.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libitkjpeg12.dylib
>>>>>>>>> 0x444000 - 0x47afff libitkjpeg16.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libitkjpeg16.dylib
>>>>>>>>> 0x483000 - 0x4affff libitkpng.dylib /Applications/
>>>>>>>>> itk_binary/bin/libitkpng.dylib
>>>>>>>>> 0x4b7000 - 0x4e6fff libITKEXPAT.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libITKEXPAT.dylib
>>>>>>>>> 0x4ee000 - 0x559fff libITKAlgorithms.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libITKAlgorithms.dylib
>>>>>>>>> 0x5d7000 - 0x633fff libITKBasicFilters.dylib /
>>>>>>>>> Applications/itk_binary/bin/libITKBasicFilters.dylib
>>>>>>>>> 0x69e000 - 0x6fbfff libITKStatistics.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libITKStatistics.dylib
>>>>>>>>> 0x766000 - 0x79cfff libitkjpeg8.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libitkjpeg8.dylib
>>>>>>>>> 0x1008000 - 0x1068fff libitktiff.dylib /Applications/
>>>>>>>>> itk_binary/bin/libitktiff.dylib
>>>>>>>>> 0x1190000 - 0x1197fff alex_lagutin.audio_hijack.server
>>>>>>>>> 1.2.9 /Library/Application Enhancers/Instant Hijack
>>>>>>>>> Server.ape/ Contents/MacOS/Instant Hijack Server
>>>>>>>>> 0x11cd000 - 0x126efff libITKSpatialObject.dylib /
>>>>>>>>> Applications/itk_binary/bin/libITKSpatialObject.dylib
>>>>>>>>> 0x134c000 - 0x1365fff GLDriver
>>>>>>>>> /System/Library/Frameworks/
>>>>>>>>> OpenGL.framework/Versions/A/Resources/ GLDriver.bundle/GLDriver
>>>>>>>>> 0x1384000 - 0x1536fff libITKCommon.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libITKCommon.dylib
>>>>>>>>> 0x1700000 - 0x189afff libITKIO.dylib /Applications/
>>>>>>>>> itk_binary/bin/libITKIO.dylib
>>>>>>>>> 0x1a49000 - 0x1b4cfff libitkgdcm.dylib /Applications/
>>>>>>>>> itk_binary/bin/libitkgdcm.dylib
>>>>>>>>> 0x1c44000 - 0x1c96fff libitkvcl.dylib /Applications/
>>>>>>>>> itk_binary/bin/libitkvcl.dylib
>>>>>>>>> 0x1d73000 - 0x1d8dfff GLRendererFloat
>>>>>>>>> /System/Library/
>>>>>>>>> Frameworks/OpenGL.framework/Versions/A/Resources/
>>>>>>>>> GLRendererFloat.bundle/GLRendererFloat
>>>>>>>>> 0x1dc8000 - 0x1e89fff libITKNumerics.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libITKNumerics.dylib
>>>>>>>>> 0x1f4d000 - 0x2005fff libitkvnl_inst.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libitkvnl_inst.dylib
>>>>>>>>> 0x20ba000 - 0x2174fff libitkvnl_algo.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libitkvnl_algo.dylib
>>>>>>>>> 0x2229000 - 0x2298fff libitksys.dylib /Applications/
>>>>>>>>> itk_binary/bin/libitksys.dylib
>>>>>>>>> 0x23b5000 - 0x2520fff libitknetlib.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libitknetlib.dylib
>>>>>>>>> 0x2563000 - 0x25fdfff libITKDICOMParser.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libITKDICOMParser.dylib
>>>>>>>>> 0x26de000 - 0x27a5fff libITKMetaIO.dylib
>>>>>>>>> /Applications/ itk_binary/bin/libITKMetaIO.dylib
>>>>>>>>> 0x28d4000 - 0x2c56fff libitkvnl.dylib /Applications/
>>>>>>>>> itk_binary/bin/libitkvnl.dylib
>>>>>>>>> 0x5dac000 - 0x5ea1fff GLEngine
>>>>>>>>> /System/Library/Frameworks/
>>>>>>>>> OpenGL.framework/Resources/GLEngine.bundle/ GLEngine
>>>>>>>>> 0x5f8a000 - 0x6060fff ATIRadeon9700GLDriver
>>>>>>>>> /System/Library/
>>>>>>>>> Extensions/ATIRadeon9700GLDriver.bundle/Contents/ MacOS/
>>>>>>>>> ATIRadeon9700GLDriver
>>>>>>>>> 0x61fd000 - 0x628cfff GLRasterARGB8888D32
>>>>>>>>> /System/Library/ Frameworks/OpenGL.framework/Resources/
>>>>>>>>> GLRasterARGB8888D32.bundle/ GLRasterARGB8888D32
>>>>>>>>> 0x80830000 - 0x8090efff libxml2.2.dylib
>>>>>>>>> /usr/lib/libxml2.2.dylib
>>>>>>>>> 0x8134c000 - 0x8134dfff libGLSystem.dylib
>>>>>>>>> /System/Library/
>>>>>>>>> Frameworks/OpenGL.framework/Versions/A/Libraries/
>>>>>>>>> libGLSystem.dylib
>>>>>>>>> 0x83b6c000 - 0x83b78fff com.apple.agl 2.5 (AGL-2.5)
>>>>>>>>> /System/ Library/Frameworks/AGL.framework/Versions/A/AGL
>>>>>>>>> 0x84cab000 - 0x84d9cfff libGLProgrammability.dylib
>>>>>>>>> /System/
>>>>>>>>> Library/Frameworks/OpenGL.framework/Versions/A/Libraries/
>>>>>>>>> libGLProgrammability.dylib
>>>>>>>>> 0x8fe00000 - 0x8fe4ffff dyld /usr/lib/dyld
>>>>>>>>> 0x90000000 - 0x9014ffff libSystem.B.dylib /usr/lib/
>>>>>>>>> libSystem.B.dylib
>>>>>>>>> 0x901c0000 - 0x9026dfff com.apple.CoreFoundation 6.3.8
>>>>>>>>> (299.36)
>>>>>>>>> /System/Library/Frameworks/CoreFoundation.framework/
>>>>>>>>> Versions/ A/CoreFoundation
>>>>>>>>> 0x902b0000 - 0x90529fff com.apple.CoreServices.CarbonCore
>>>>>>>>> 10.3.7 /System/Library/Frameworks/CoreServices.framework/
>>>>>>>>> Versions/A/
>>>>>>>>> Frameworks/CarbonCore.framework/Versions/A/CarbonCore
>>>>>>>>> 0x90584000 - 0x905f3fff com.apple.framework.IOKit 1.3.6
>>>>>>>>> (???) /
>>>>>>>>> System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
>>>>>>>>> 0x90610000 - 0x9069afff com.apple.CoreServices.OSServices
>>>>>>>>> 3.0.1 /System/Library/Frameworks/CoreServices.framework/
>>>>>>>>> Versions/A/
>>>>>>>>> Frameworks/OSServices.framework/Versions/A/OSServices
>>>>>>>>> 0x90700000 - 0x90700fff com.apple.CoreServices 10.3 (???)
>>>>>>>>> /
>>>>>>>>> System/Library/Frameworks/CoreServices.framework/Versions/A/
>>>>>>>>> CoreServices
>>>>>>>>> 0x90702000 - 0x90769fff com.apple.audio.CoreAudio 2.1.3
>>>>>>>>> /
>>>>>>>>> System/Library/Frameworks/CoreAudio.framework/Versions/A/
>>>>>>>>> CoreAudio
>>>>>>>>> 0xc0000000 - 0xc000ffff com.unsanity.ape 1.4.6 /Library/
>>>>>>>>> Frameworks/ApplicationEnhancer.framework/Versions/A/
>>>>>>>>> ApplicationEnhancer
>>>>>>>>> ----------------------------------------------------------------
>>>>>>>>> -- -- - --- -----------
>>>>>>>>> Pavel Tomancak, Ph.D.
>>>>>>>>> Group Leader
>>>>>>>>> Max Planck Institute of Molecular Cell Biology and Genetics
>>>>>>>>> Pfotenhauerstr. 108
>>>>>>>>> D-01307 Dresden Tel.: +49 351 210 2670
>>>>>>>>> Germany Fax: +49 351 210 2020
>>>>>>>>> tomancak at mpi-cbg.de
>>>>>>>>> http://www.mpi-cbg.de
>>>>>>>>> ----------------------------------------------------------------
>>>>>>>>> -- -- - --- -----------
>>>>>>>>> _______________________________________________
>>>>>>>>> Insight-users mailing list
>>>>>>>>> Insight-users at itk.org
>>>>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>>
>
>
>
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