Hi Brige,
I am not someone who has had success (or failures) with mouse brain
segmentation, but I tried segmenting the map015 left hemisphere using
Caret, just to see what would happen. I made these selections:
* left the voxel size at 0.056mm
* GMpeak=45 ; WMpeak 60
* toggled off disconnect eye and skull and disconnect hindbrain, since
these have no chance of working on rodents
* toggled on generate segmentation
* toggled off fill ventricles, automatic error correction, and all
remaining options
The idea was to see if I could get an initial segmentation without going
any further. The progress bar showed it was working on inner boundary
(25%), but then Caret crashed with the following gdb stack trace:
Starting program: /146Gb/caret/bin/caret5
[Thread debugging using libthread_db enabled]
[New Thread 1085958368 (LWP 14035)]
Set the environment variables CARET_DEBUG for debugging information.
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 1085958368 (LWP 14035)]
0x08624da2 in VolumeFile::copyVolumeData (this=0xbfffa640, [EMAIL PROTECTED])
at VolumeFile.cxx:194
194 VolumeFile.cxx: No such file or directory.
in VolumeFile.cxx
(gdb) where
#0 0x08624da2 in VolumeFile::copyVolumeData (this=0xbfffa640, [EMAIL
PROTECTED])
at VolumeFile.cxx:194
#1 0x0862428c in VolumeFile::operator= (this=0xbfffa640, [EMAIL PROTECTED])
at VolumeFile.cxx:127
#2 0x0848ca87 in
BrainModelVolumeSureFitSegmentation::generateInnerBoundary
(this=0xbfffb550) at BrainModelVolumeSureFitSegmentation.cxx:2606
#3 0x0847e9cc in BrainModelVolumeSureFitSegmentation::execute (
this=0xbfffb550) at BrainModelVolumeSureFitSegmentation.cxx:421
#4 0x083312d1 in
GuiVolumeSureFitSegmentationDialog::performSegmentation (this=0x9800808)
at GuiVolumeSureFitSegmentationDialog.cxx:1405
#5 0x0832e018 in GuiVolumeSureFitSegmentationDialog::next (
this=0x9800808) at GuiVolumeSureFitSegmentationDialog.cxx:936
#6 0x08af5611 in QWizard::qt_invoke ()
at /usr/local/qt/include/qrect.h:247
#7 0x08351677 in GuiVolumeSureFitSegmentationDialog::qt_invoke (
this=0x9800808, _id=56, _o=0xbfffc990)
at moc_GuiVolumeSureFitSegmentationDialog.cpp:114
#8 0x0889ac64 in QObject::activate_signal ()
at /usr/local/qt/include/qrect.h:247
#9 0x0889a9fb in QObject::activate_signal ()
at /usr/local/qt/include/qrect.h:247
#10 0x08adcf3e in QButton::clicked ()
at /usr/local/qt/include/qrect.h:247
#11 0x089120bd in QButton::mouseReleaseEvent ()
at /usr/local/qt/include/qrect.h:247
#12 0x088c34ed in QWidget::event ()
at /usr/local/qt/include/qrect.h:247
#13 0x088592bd in QApplication::internalNotify ()
at /usr/local/qt/include/qrect.h:247
#14 0x08858a90 in QApplication::notify ()
at /usr/local/qt/include/qrect.h:247
#15 0x08802e6c in QETWidget::translateMouseEvent ()
at /usr/local/qt/include/qrect.h:247
#16 0x08800eaf in QApplication::x11ProcessEvent ()
at /usr/local/qt/include/qrect.h:247
#17 0x08afb638 in QEventLoop::processEvents ()
at /usr/local/qt/include/qrect.h:247
#18 0x088637af in QEventLoop::enterLoop ()
at /usr/local/qt/include/qrect.h:247
#19 0x08863684 in QEventLoop::exec ()
at /usr/local/qt/include/qrect.h:247
#20 0x088594a3 in QApplication::exec ()
at /usr/local/qt/include/qrect.h:247
#21 0x08336918 in main (argc=1, argv=0xbfffe264) at main.cxx:554
(gdb)
I knew there were crashing problems when toggling off disconnect
hindbrain, but I didn't know what would happen when the other options
were also toggled off.
We need to look at this and get it working. The idea is to replicate
the functionality SureFit had with these selections:
segment full volume
fill ventricles no
skip error correction
review surface first
skip sulci identification
But I don't know how long this will take. Meanwhile, if you're running
Linux, you might try using SureFit for this purpose, using the settings
above (after doing volume preparation -- orientation, setting AC,
cropping, and setting peaks).
Donna
On 07/29/2005 01:51 PM, Brige Chugh wrote:
Hi,
I have been trying to apply caret's automatic segmentation routine on
the mouse brain. I have registered and resampled the brain so that it
is similar to the map015 atlas and have performed n3 correction. I am
following the caret segmentation tutorial closely. I am able to
clearly discern the grey and white matter peaks but I have found that
when I try to run automatic segmentation, it always crashes. The
program closes and I get the message "segmentation fault". As I new
user to the caret environment, I would really appreciate any advice
from anyone who has had some success with mouse brain segmentation.
Thanks in advance,
Brige Paul
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