bad allocation error in FastMarchingSegmentation module

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

bad allocation error in FastMarchingSegmentation module

אלעד-2
hello all,

I have a problem with the FastMarchingSegmentation module,
when i use it after loading Slicer with a volume and some input the module works great.
but if i try to use it again, i receive a bad allocation error. i guess there is a memory leak in this module.

can someone tell us what can be done, this module is very important for our work.

Thank you,
Elad Dabool



the error we received:

ERROR: In ..\KWWidgets\vtkKWTkUtilities.
cxx, line 230
vtkSlicerApplication (0BD9AF90):
    Script:
FastMarchingSegmentationProcessGUIEvents vtkObj5152 vtkObj5265 10000
    Returned Error on line 1:
Uncaught exception: bad allocation

Stack trace:
Uncaught exception: bad allocation

    while executing
"$fmFilter init [expr [lindex $dim 1] + 1] [expr [lindex $dim 3] + 1]  [expr [lindex $dim 5] + 1] $depth $dx $dy $dz"
    (procedure "FastMarchingSegmentationInitializeFilter" line 29)
    invoked from within
"FastMarchingSegmentationInitializeFilter $this"
    (procedure "FastMarchingSegmentationProcessGUIEvents" line 43)
    invoked from within
"FastMarchingSegmentationProcessGUIEvents vtkObj5152 vtkObj5265 10000"


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: bad allocation error in FastMarchingSegmentation module

Andrey Fedorov
Elad,

I doubt the error is caused by a memory leak.

What is the range of intensities that you have in your input image,
and what are the dimensions in voxel space?

The code allocates quite a lot of memory (my fault, this is not
described in the documentation). The function that caused the failure
in your case attempts to allocate something like

17*dX*dY*dZ + 20*(max_intensity-min_intensity) bytes (if you use 32-bit system)

where dX dY dZ are the dimensions of the input image in voxel space.

So, depending on what is the size of your image, you may run out of
memory, which would cause the problem you describe. Chances of this
happening depend on the size of the image, scalar type, scalar range,
OS you use, whether you use 32- or 64- bit system, and how much memory
you already have in use. You did not give any details of your setup,
so it's hard to pin-point the problem.

There are several approaches to resolve this, without looking at your setup:

1) you can use CropVolume module
(http://wiki.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6)
to extract a smaller VOI around the structure you are trying to
segment (use resample constant 1.0). This will reduce dimensions of
the input image.

2) you can rescale the intensities of your image to a smaller range

3) you can do both 1) and 2)

Unfortunately, there is no module in Slicer to do (2). I can add this
module, if (1) does not work for you.

Please let us know if this helps you at all.

Also, if your data is anonymized,and you can share it, please share it
with me, and I could try to give you more specific help.

AF



On Wed, May 19, 2010 at 15:10, אלעד <[hidden email]> wrote:

> hello all,
>
> I have a problem with the FastMarchingSegmentation module,
> when i use it after loading Slicer with a volume and some input the module
> works great.
> but if i try to use it again, i receive a bad allocation error. i guess
> there is a memory leak in this module.
>
> can someone tell us what can be done, this module is very important for our
> work.
>
> Thank you,
> Elad Dabool
>
>
>
> the error we received:
>
> ERROR: In ..\KWWidgets\vtkKWTkUtilities.
> cxx, line 230
> vtkSlicerApplication (0BD9AF90):
>     Script:
> FastMarchingSegmentationProcessGUIEvents vtkObj5152 vtkObj5265 10000
>     Returned Error on line 1:
> Uncaught exception: bad allocation
>
> Stack trace:
> Uncaught exception: bad allocation
>
>     while executing
> "$fmFilter init [expr [lindex $dim 1] + 1] [expr [lindex $dim 3] + 1]  [expr
> [lindex $dim 5] + 1] $depth $dx $dy $dz"
>     (procedure "FastMarchingSegmentationInitializeFilter" line 29)
>     invoked from within
> "FastMarchingSegmentationInitializeFilter $this"
>     (procedure "FastMarchingSegmentationProcessGUIEvents" line 43)
>     invoked from within
> "FastMarchingSegmentationProcessGUIEvents vtkObj5152 vtkObj5265 10000"
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
>
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: bad allocation error in FastMarchingSegmentation module

Andrey Fedorov
On Wed, May 19, 2010 at 15:57, Andriy Fedorov <[hidden email]> wrote:
> I doubt the error is caused by a memory leak.
>

I take this back.

Currently, there is no test that verifies that this module is actually
leak-free. Since the memory requirements are indeed quite high,
repetitive application of this module can potentially exhaust your
memory, if there are leaks.

I will submit a bug to Mantis to add testing of this feature of the
code. Meanwhile, you can try to segment the image first thing after
opening Slicer. If the problem persists, it probably is not caused by
a memory leak.



> What is the range of intensities that you have in your input image,
> and what are the dimensions in voxel space?
>
> The code allocates quite a lot of memory (my fault, this is not
> described in the documentation). The function that caused the failure
> in your case attempts to allocate something like
>
> 17*dX*dY*dZ + 20*(max_intensity-min_intensity) bytes (if you use 32-bit system)
>
> where dX dY dZ are the dimensions of the input image in voxel space.
>
> So, depending on what is the size of your image, you may run out of
> memory, which would cause the problem you describe. Chances of this
> happening depend on the size of the image, scalar type, scalar range,
> OS you use, whether you use 32- or 64- bit system, and how much memory
> you already have in use. You did not give any details of your setup,
> so it's hard to pin-point the problem.
>
> There are several approaches to resolve this, without looking at your setup:
>
> 1) you can use CropVolume module
> (http://wiki.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6)
> to extract a smaller VOI around the structure you are trying to
> segment (use resample constant 1.0). This will reduce dimensions of
> the input image.
>
> 2) you can rescale the intensities of your image to a smaller range
>
> 3) you can do both 1) and 2)
>
> Unfortunately, there is no module in Slicer to do (2). I can add this
> module, if (1) does not work for you.
>
> Please let us know if this helps you at all.
>
> Also, if your data is anonymized,and you can share it, please share it
> with me, and I could try to give you more specific help.
>
> AF
>
>
>
> On Wed, May 19, 2010 at 15:10, אלעד <[hidden email]> wrote:
>> hello all,
>>
>> I have a problem with the FastMarchingSegmentation module,
>> when i use it after loading Slicer with a volume and some input the module
>> works great.
>> but if i try to use it again, i receive a bad allocation error. i guess
>> there is a memory leak in this module.
>>
>> can someone tell us what can be done, this module is very important for our
>> work.
>>
>> Thank you,
>> Elad Dabool
>>
>>
>>
>> the error we received:
>>
>> ERROR: In ..\KWWidgets\vtkKWTkUtilities.
>> cxx, line 230
>> vtkSlicerApplication (0BD9AF90):
>>     Script:
>> FastMarchingSegmentationProcessGUIEvents vtkObj5152 vtkObj5265 10000
>>     Returned Error on line 1:
>> Uncaught exception: bad allocation
>>
>> Stack trace:
>> Uncaught exception: bad allocation
>>
>>     while executing
>> "$fmFilter init [expr [lindex $dim 1] + 1] [expr [lindex $dim 3] + 1]  [expr
>> [lindex $dim 5] + 1] $depth $dx $dy $dz"
>>     (procedure "FastMarchingSegmentationInitializeFilter" line 29)
>>     invoked from within
>> "FastMarchingSegmentationInitializeFilter $this"
>>     (procedure "FastMarchingSegmentationProcessGUIEvents" line 43)
>>     invoked from within
>> "FastMarchingSegmentationProcessGUIEvents vtkObj5152 vtkObj5265 10000"
>>
>>
>> _______________________________________________
>> slicer-users mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> To unsubscribe: send email to [hidden email]
>> with unsubscribe as the subject
>>
>
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: bad allocation error in FastMarchingSegmentation module

Andrey Fedorov
On Thu, May 20, 2010 at 01:12, אלעד <[hidden email]> wrote:
> It will be great if you tell me how i can keep track on this bug.

Elad, I will update this thread when it is resolved, or when I have a
better understanding what's going on. The bug is here
http://na-mic.org/Mantis/view.php?id=854

Just to make sure -- the module fails when you try to use it with the
exact same image repeatedly, correct?

My initial understanding of your email was that you can use the module
for some images, but not for some other images.

> you are right that this module consumes a lot of memory, but as you said, if
> it works the first time and then fails,
> memory leak is probably the reason.
>
> unfortunately, rescaling the image is not an option for us as well as
> reducing its intensities
> so we will have to wait for this bug fix.
>
> Elad Dabool
>
> On Wed, May 19, 2010 at 11:08 PM, Andriy Fedorov <[hidden email]>
> wrote:
>>
>> On Wed, May 19, 2010 at 15:57, Andriy Fedorov <[hidden email]>
>> wrote:
>> > I doubt the error is caused by a memory leak.
>> >
>>
>> I take this back.
>>
>> Currently, there is no test that verifies that this module is actually
>> leak-free. Since the memory requirements are indeed quite high,
>> repetitive application of this module can potentially exhaust your
>> memory, if there are leaks.
>>
>> I will submit a bug to Mantis to add testing of this feature of the
>> code. Meanwhile, you can try to segment the image first thing after
>> opening Slicer. If the problem persists, it probably is not caused by
>> a memory leak.
>>
>>
>>
>> > What is the range of intensities that you have in your input image,
>> > and what are the dimensions in voxel space?
>> >
>> > The code allocates quite a lot of memory (my fault, this is not
>> > described in the documentation). The function that caused the failure
>> > in your case attempts to allocate something like
>> >
>> > 17*dX*dY*dZ + 20*(max_intensity-min_intensity) bytes (if you use 32-bit
>> > system)
>> >
>> > where dX dY dZ are the dimensions of the input image in voxel space.
>> >
>> > So, depending on what is the size of your image, you may run out of
>> > memory, which would cause the problem you describe. Chances of this
>> > happening depend on the size of the image, scalar type, scalar range,
>> > OS you use, whether you use 32- or 64- bit system, and how much memory
>> > you already have in use. You did not give any details of your setup,
>> > so it's hard to pin-point the problem.
>> >
>> > There are several approaches to resolve this, without looking at your
>> > setup:
>> >
>> > 1) you can use CropVolume module
>> >
>> > (http://wiki.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6)
>> > to extract a smaller VOI around the structure you are trying to
>> > segment (use resample constant 1.0). This will reduce dimensions of
>> > the input image.
>> >
>> > 2) you can rescale the intensities of your image to a smaller range
>> >
>> > 3) you can do both 1) and 2)
>> >
>> > Unfortunately, there is no module in Slicer to do (2). I can add this
>> > module, if (1) does not work for you.
>> >
>> > Please let us know if this helps you at all.
>> >
>> > Also, if your data is anonymized,and you can share it, please share it
>> > with me, and I could try to give you more specific help.
>> >
>> > AF
>> >
>> >
>> >
>> > On Wed, May 19, 2010 at 15:10, אלעד <[hidden email]> wrote:
>> >> hello all,
>> >>
>> >> I have a problem with the FastMarchingSegmentation module,
>> >> when i use it after loading Slicer with a volume and some input the
>> >> module
>> >> works great.
>> >> but if i try to use it again, i receive a bad allocation error. i guess
>> >> there is a memory leak in this module.
>> >>
>> >> can someone tell us what can be done, this module is very important for
>> >> our
>> >> work.
>> >>
>> >> Thank you,
>> >> Elad Dabool
>> >>
>> >>
>> >>
>> >> the error we received:
>> >>
>> >> ERROR: In ..\KWWidgets\vtkKWTkUtilities.
>> >> cxx, line 230
>> >> vtkSlicerApplication (0BD9AF90):
>> >>     Script:
>> >> FastMarchingSegmentationProcessGUIEvents vtkObj5152 vtkObj5265 10000
>> >>     Returned Error on line 1:
>> >> Uncaught exception: bad allocation
>> >>
>> >> Stack trace:
>> >> Uncaught exception: bad allocation
>> >>
>> >>     while executing
>> >> "$fmFilter init [expr [lindex $dim 1] + 1] [expr [lindex $dim 3] + 1]
>> >> [expr
>> >> [lindex $dim 5] + 1] $depth $dx $dy $dz"
>> >>     (procedure "FastMarchingSegmentationInitializeFilter" line 29)
>> >>     invoked from within
>> >> "FastMarchingSegmentationInitializeFilter $this"
>> >>     (procedure "FastMarchingSegmentationProcessGUIEvents" line 43)
>> >>     invoked from within
>> >> "FastMarchingSegmentationProcessGUIEvents vtkObj5152 vtkObj5265 10000"
>> >>
>> >>
>> >> _______________________________________________
>> >> slicer-users mailing list
>> >> [hidden email]
>> >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> >> To unsubscribe: send email to
>> >> [hidden email]
>> >> with unsubscribe as the subject
>> >>
>> >
>
>
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: bad allocation error in FastMarchingSegmentation module

Andrey Fedorov
Hi Elad,

I am still struggling with the test, but I did find the place where I
think most of the memory was leaked.

I fixed this in the trunk and in the 3.6 branch. If you use Slicer
built from the source code, you should be able to update the source
and rebuild to test the change. If you use binary builds, try the
nightly build tomorrow.

Please let me know if the fix I committed solved the problem you had before.

Thank you very much for reporting this problem!

AF


On Thu, May 20, 2010 at 08:49, Andriy Fedorov <[hidden email]> wrote:

> On Thu, May 20, 2010 at 01:12, אלעד <[hidden email]> wrote:
>> It will be great if you tell me how i can keep track on this bug.
>
> Elad, I will update this thread when it is resolved, or when I have a
> better understanding what's going on. The bug is here
> http://na-mic.org/Mantis/view.php?id=854
>
> Just to make sure -- the module fails when you try to use it with the
> exact same image repeatedly, correct?
>
> My initial understanding of your email was that you can use the module
> for some images, but not for some other images.
>
>> you are right that this module consumes a lot of memory, but as you said, if
>> it works the first time and then fails,
>> memory leak is probably the reason.
>>
>> unfortunately, rescaling the image is not an option for us as well as
>> reducing its intensities
>> so we will have to wait for this bug fix.
>>
>> Elad Dabool
>>
>> On Wed, May 19, 2010 at 11:08 PM, Andriy Fedorov <[hidden email]>
>> wrote:
>>>
>>> On Wed, May 19, 2010 at 15:57, Andriy Fedorov <[hidden email]>
>>> wrote:
>>> > I doubt the error is caused by a memory leak.
>>> >
>>>
>>> I take this back.
>>>
>>> Currently, there is no test that verifies that this module is actually
>>> leak-free. Since the memory requirements are indeed quite high,
>>> repetitive application of this module can potentially exhaust your
>>> memory, if there are leaks.
>>>
>>> I will submit a bug to Mantis to add testing of this feature of the
>>> code. Meanwhile, you can try to segment the image first thing after
>>> opening Slicer. If the problem persists, it probably is not caused by
>>> a memory leak.
>>>
>>>
>>>
>>> > What is the range of intensities that you have in your input image,
>>> > and what are the dimensions in voxel space?
>>> >
>>> > The code allocates quite a lot of memory (my fault, this is not
>>> > described in the documentation). The function that caused the failure
>>> > in your case attempts to allocate something like
>>> >
>>> > 17*dX*dY*dZ + 20*(max_intensity-min_intensity) bytes (if you use 32-bit
>>> > system)
>>> >
>>> > where dX dY dZ are the dimensions of the input image in voxel space.
>>> >
>>> > So, depending on what is the size of your image, you may run out of
>>> > memory, which would cause the problem you describe. Chances of this
>>> > happening depend on the size of the image, scalar type, scalar range,
>>> > OS you use, whether you use 32- or 64- bit system, and how much memory
>>> > you already have in use. You did not give any details of your setup,
>>> > so it's hard to pin-point the problem.
>>> >
>>> > There are several approaches to resolve this, without looking at your
>>> > setup:
>>> >
>>> > 1) you can use CropVolume module
>>> >
>>> > (http://wiki.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6)
>>> > to extract a smaller VOI around the structure you are trying to
>>> > segment (use resample constant 1.0). This will reduce dimensions of
>>> > the input image.
>>> >
>>> > 2) you can rescale the intensities of your image to a smaller range
>>> >
>>> > 3) you can do both 1) and 2)
>>> >
>>> > Unfortunately, there is no module in Slicer to do (2). I can add this
>>> > module, if (1) does not work for you.
>>> >
>>> > Please let us know if this helps you at all.
>>> >
>>> > Also, if your data is anonymized,and you can share it, please share it
>>> > with me, and I could try to give you more specific help.
>>> >
>>> > AF
>>> >
>>> >
>>> >
>>> > On Wed, May 19, 2010 at 15:10, אלעד <[hidden email]> wrote:
>>> >> hello all,
>>> >>
>>> >> I have a problem with the FastMarchingSegmentation module,
>>> >> when i use it after loading Slicer with a volume and some input the
>>> >> module
>>> >> works great.
>>> >> but if i try to use it again, i receive a bad allocation error. i guess
>>> >> there is a memory leak in this module.
>>> >>
>>> >> can someone tell us what can be done, this module is very important for
>>> >> our
>>> >> work.
>>> >>
>>> >> Thank you,
>>> >> Elad Dabool
>>> >>
>>> >>
>>> >>
>>> >> the error we received:
>>> >>
>>> >> ERROR: In ..\KWWidgets\vtkKWTkUtilities.
>>> >> cxx, line 230
>>> >> vtkSlicerApplication (0BD9AF90):
>>> >>     Script:
>>> >> FastMarchingSegmentationProcessGUIEvents vtkObj5152 vtkObj5265 10000
>>> >>     Returned Error on line 1:
>>> >> Uncaught exception: bad allocation
>>> >>
>>> >> Stack trace:
>>> >> Uncaught exception: bad allocation
>>> >>
>>> >>     while executing
>>> >> "$fmFilter init [expr [lindex $dim 1] + 1] [expr [lindex $dim 3] + 1]
>>> >> [expr
>>> >> [lindex $dim 5] + 1] $depth $dx $dy $dz"
>>> >>     (procedure "FastMarchingSegmentationInitializeFilter" line 29)
>>> >>     invoked from within
>>> >> "FastMarchingSegmentationInitializeFilter $this"
>>> >>     (procedure "FastMarchingSegmentationProcessGUIEvents" line 43)
>>> >>     invoked from within
>>> >> "FastMarchingSegmentationProcessGUIEvents vtkObj5152 vtkObj5265 10000"
>>> >>
>>> >>
>>> >> _______________________________________________
>>> >> slicer-users mailing list
>>> >> [hidden email]
>>> >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>>> >> To unsubscribe: send email to
>>> >> [hidden email]
>>> >> with unsubscribe as the subject
>>> >>
>>> >
>>
>>
>
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: bad allocation error in FastMarchingSegmentation module

Andrey Fedorov
Elad,

Just to update this topic -- I did add a test that exercises
functionality of the fast marching VTK class. The test cleared the
dashboard

http://www.cdash.org/CDash/testSummary.php?project=20&name=FastMarchingTest2&date=2010-05-21

(the failing sites have problems unrelated to the test). Also I did a
valgrind test locally (valgrind reports all memory leaks, unlike
dashboard, which reports only VTK objects that have not been
deallocated), and it did not report memory leaks.

I hope the problem you had has been resolved.

AF



On Thu, May 20, 2010 at 11:32, Andriy Fedorov <[hidden email]> wrote:

> Hi Elad,
>
> I am still struggling with the test, but I did find the place where I
> think most of the memory was leaked.
>
> I fixed this in the trunk and in the 3.6 branch. If you use Slicer
> built from the source code, you should be able to update the source
> and rebuild to test the change. If you use binary builds, try the
> nightly build tomorrow.
>
> Please let me know if the fix I committed solved the problem you had before.
>
> Thank you very much for reporting this problem!
>
> AF
>
>
> On Thu, May 20, 2010 at 08:49, Andriy Fedorov <[hidden email]> wrote:
>> On Thu, May 20, 2010 at 01:12, אלעד <[hidden email]> wrote:
>>> It will be great if you tell me how i can keep track on this bug.
>>
>> Elad, I will update this thread when it is resolved, or when I have a
>> better understanding what's going on. The bug is here
>> http://na-mic.org/Mantis/view.php?id=854
>>
>> Just to make sure -- the module fails when you try to use it with the
>> exact same image repeatedly, correct?
>>
>> My initial understanding of your email was that you can use the module
>> for some images, but not for some other images.
>>
>>> you are right that this module consumes a lot of memory, but as you said, if
>>> it works the first time and then fails,
>>> memory leak is probably the reason.
>>>
>>> unfortunately, rescaling the image is not an option for us as well as
>>> reducing its intensities
>>> so we will have to wait for this bug fix.
>>>
>>> Elad Dabool
>>>
>>> On Wed, May 19, 2010 at 11:08 PM, Andriy Fedorov <[hidden email]>
>>> wrote:
>>>>
>>>> On Wed, May 19, 2010 at 15:57, Andriy Fedorov <[hidden email]>
>>>> wrote:
>>>> > I doubt the error is caused by a memory leak.
>>>> >
>>>>
>>>> I take this back.
>>>>
>>>> Currently, there is no test that verifies that this module is actually
>>>> leak-free. Since the memory requirements are indeed quite high,
>>>> repetitive application of this module can potentially exhaust your
>>>> memory, if there are leaks.
>>>>
>>>> I will submit a bug to Mantis to add testing of this feature of the
>>>> code. Meanwhile, you can try to segment the image first thing after
>>>> opening Slicer. If the problem persists, it probably is not caused by
>>>> a memory leak.
>>>>
>>>>
>>>>
>>>> > What is the range of intensities that you have in your input image,
>>>> > and what are the dimensions in voxel space?
>>>> >
>>>> > The code allocates quite a lot of memory (my fault, this is not
>>>> > described in the documentation). The function that caused the failure
>>>> > in your case attempts to allocate something like
>>>> >
>>>> > 17*dX*dY*dZ + 20*(max_intensity-min_intensity) bytes (if you use 32-bit
>>>> > system)
>>>> >
>>>> > where dX dY dZ are the dimensions of the input image in voxel space.
>>>> >
>>>> > So, depending on what is the size of your image, you may run out of
>>>> > memory, which would cause the problem you describe. Chances of this
>>>> > happening depend on the size of the image, scalar type, scalar range,
>>>> > OS you use, whether you use 32- or 64- bit system, and how much memory
>>>> > you already have in use. You did not give any details of your setup,
>>>> > so it's hard to pin-point the problem.
>>>> >
>>>> > There are several approaches to resolve this, without looking at your
>>>> > setup:
>>>> >
>>>> > 1) you can use CropVolume module
>>>> >
>>>> > (http://wiki.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6)
>>>> > to extract a smaller VOI around the structure you are trying to
>>>> > segment (use resample constant 1.0). This will reduce dimensions of
>>>> > the input image.
>>>> >
>>>> > 2) you can rescale the intensities of your image to a smaller range
>>>> >
>>>> > 3) you can do both 1) and 2)
>>>> >
>>>> > Unfortunately, there is no module in Slicer to do (2). I can add this
>>>> > module, if (1) does not work for you.
>>>> >
>>>> > Please let us know if this helps you at all.
>>>> >
>>>> > Also, if your data is anonymized,and you can share it, please share it
>>>> > with me, and I could try to give you more specific help.
>>>> >
>>>> > AF
>>>> >
>>>> >
>>>> >
>>>> > On Wed, May 19, 2010 at 15:10, אלעד <[hidden email]> wrote:
>>>> >> hello all,
>>>> >>
>>>> >> I have a problem with the FastMarchingSegmentation module,
>>>> >> when i use it after loading Slicer with a volume and some input the
>>>> >> module
>>>> >> works great.
>>>> >> but if i try to use it again, i receive a bad allocation error. i guess
>>>> >> there is a memory leak in this module.
>>>> >>
>>>> >> can someone tell us what can be done, this module is very important for
>>>> >> our
>>>> >> work.
>>>> >>
>>>> >> Thank you,
>>>> >> Elad Dabool
>>>> >>
>>>> >>
>>>> >>
>>>> >> the error we received:
>>>> >>
>>>> >> ERROR: In ..\KWWidgets\vtkKWTkUtilities.
>>>> >> cxx, line 230
>>>> >> vtkSlicerApplication (0BD9AF90):
>>>> >>     Script:
>>>> >> FastMarchingSegmentationProcessGUIEvents vtkObj5152 vtkObj5265 10000
>>>> >>     Returned Error on line 1:
>>>> >> Uncaught exception: bad allocation
>>>> >>
>>>> >> Stack trace:
>>>> >> Uncaught exception: bad allocation
>>>> >>
>>>> >>     while executing
>>>> >> "$fmFilter init [expr [lindex $dim 1] + 1] [expr [lindex $dim 3] + 1]
>>>> >> [expr
>>>> >> [lindex $dim 5] + 1] $depth $dx $dy $dz"
>>>> >>     (procedure "FastMarchingSegmentationInitializeFilter" line 29)
>>>> >>     invoked from within
>>>> >> "FastMarchingSegmentationInitializeFilter $this"
>>>> >>     (procedure "FastMarchingSegmentationProcessGUIEvents" line 43)
>>>> >>     invoked from within
>>>> >> "FastMarchingSegmentationProcessGUIEvents vtkObj5152 vtkObj5265 10000"
>>>> >>
>>>> >>
>>>> >> _______________________________________________
>>>> >> slicer-users mailing list
>>>> >> [hidden email]
>>>> >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>>>> >> To unsubscribe: send email to
>>>> >> [hidden email]
>>>> >> with unsubscribe as the subject
>>>> >>
>>>> >
>>>
>>>
>>
>
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject