debuging crashing itksnap under linux

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Dr. Roman Grothausmann

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Sep 3, 2013, 8:08:57 AM9/3/13

to itksna...@googlegroups.com

Dear mailing list members,

We've been using itksnap (2.2.0 and 2.4.0) under windows for some time now and
it crashed very rarely. Now since we got bigger dataset that we want to segment
with the snake tool we run out of memory. Therefore we want to use itksnap on a
server running linux with lots of RAM but there both the pre-compiled versions
of itksnap (2.2.0, 2.4.0, 2.5.0-alpha) and also self-build ones (2.4.0, 2.4.2 or
qtsnap) crash within a few minutes of usage and/or the snake tool runs very
quickly but does not change the active contour at all.
What would be the best way to debug these problems under linux?
Building itksnap from source only worked with itk-4.2.1 however itk-4.2.1 seems
not to be multi-threaded and the snake tool often does not evolve. I tried also
to link against itk-4.3 and itk-4.4 (which again are able to use multiple
threads) but it seems itksnap is not yet adjusted to the changes of the API.
Is it planned to adjust the source of itksnap to comply to itk > 4.2.1 in the
near future?

Any help or hints are very much appreciated
Roman
--
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f�r Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574

Paul Yushkevich

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Sep 3, 2013, 10:38:06 AM9/3/13

to itksna...@googlegroups.com

Hi Roman,

I have a couple of questions:

Do the linux versions crash when segmenting very large images (what size?) or any size images?

The case when the bubbles don't grow, does that occur only when the bubbles are small or for large bubbles (>10 voxels across) too?

Thanks!
Paul

On Tue, Sep 3, 2013 at 8:08 AM, Dr. Roman Grothausmann <grothausm...@mh-hannover.de> wrote:

Dear mailing list members,

We've been using itksnap (2.2.0 and 2.4.0) under windows for some time now and it crashed very rarely. Now since we got bigger dataset that we want to segment with the snake tool we run out of memory. Therefore we want to use itksnap on a server running linux with lots of RAM but there both the pre-compiled versions of itksnap (2.2.0, 2.4.0, 2.5.0-alpha) and also self-build ones (2.4.0, 2.4.2 or qtsnap) crash within a few minutes of usage and/or the snake tool runs very quickly but does not change the active contour at all.
What would be the best way to debug these problems under linux?
Building itksnap from source only worked with itk-4.2.1 however itk-4.2.1 seems not to be multi-threaded and the snake tool often does not evolve. I tried also to link against itk-4.3 and itk-4.4 (which again are able to use multiple threads) but it seems itksnap is not yet adjusted to the changes of the API.
Is it planned to adjust the source of itksnap to comply to itk > 4.2.1 in the near future?

Any help or hints are very much appreciated
Roman

--
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut für Funktionelle und Angewandte Anatomie, OE 4120

Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

Paul Yushkevich

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Sep 4, 2013, 10:28:12 AM9/4/13

to Dr. Roman Grothausmann, itksna...@googlegroups.com

Hi Roman,

I got SNAP to compile with ITK 4.4 last night, but the same problems persist. I was testing on my mac, and only had the problem with the bubble not growing if it was small, about 10 voxels across or less. This was the case for ITK 4.4 and ITK 4.2.

I will just have to figure out what changed going from older ITK to the newer ITK...

Thanks!
Paul.

On Wed, Sep 4, 2013 at 8:55 AM, Dr. Roman Grothausmann <grothausm...@mh-hannover.de> wrote:

Hi Paul,

Thanks for Your reply.

On 03/09/13 16:38, Paul Yushkevich wrote:

Do the linux versions crash when segmenting very large images (what size?) or
any size images?

The crashes did not seem to depend on the size of the loaded image. We only ran
out of RAM on the windows machines with images > 600GB.

The case when the bubbles don't grow, does that occur only when the bubbles
are small or for large bubbles (>10 voxels across) too?

Also for large bubbles (e.g. 60 voxel) and for any kind of parameter combination
we tried.

I just managed to compile 2.4.2 from git with itk-3.20.1 (needed to add
ITKIOReview to the main CMakeLists.txt) and vtk-5.10 which seems to run nicely, no crashes so far and the snake-tool uses multiple cores. I think we can live with that for now.
However it would be nice to have itksnap compile with itk>=4.3. Perhaps that would already solve the bubble problem. Is there any other reason except the changes of the API that itk>=4.3 is not yet supported?

Many thanks for Your help
Roman

Thanks! Paul

On Tue, Sep 3, 2013 at 8:08 AM, Dr. Roman Grothausmann

<grothausmann.roman@mh-hannover.de

<mailto:grothausmann.roman@mh-hannover.de>> wrote:

Dear mailing list members,

We've been using itksnap (2.2.0 and 2.4.0) under windows for some time now
and it crashed very rarely. Now since we got bigger dataset that we want to
segment with the snake tool we run out of memory. Therefore we want to use
itksnap on a server running linux with lots of RAM but there both the
pre-compiled versions of itksnap (2.2.0, 2.4.0, 2.5.0-alpha) and also
self-build ones (2.4.0, 2.4.2 or qtsnap) crash within a few minutes of usage
and/or the snake tool runs very quickly but does not change the active
contour at all. What would be the best way to debug these problems under
linux? Building itksnap from source only worked with itk-4.2.1 however
itk-4.2.1 seems not to be multi-threaded and the snake tool often does not
evolve. I tried also to link against itk-4.3 and itk-4.4 (which again are
able to use multiple threads) but it seems itksnap is not yet adjusted to
the changes of the API. Is it planned to adjust the source of itksnap to
comply to itk > 4.2.1 in the near future?

Any help or hints are very much appreciated Roman -- Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung Tomography and Digital Image
Analysis

Institut für Funktionelle und Angewandte Anatomie, OE 4120 Medizinische
Hochschule Hannover Carl-Neuberg-Str. 1 D-30625 Hannover

Tel. +49 511 532-9574 <tel:%2B49%20511%20532-9574>

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-- Paul A. Yushkevich, Ph.D. Associate Professor Penn Image Computing and
Science Laboratory Department of Radiology University of Pennsylvania

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--

Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574

Dr. Roman Grothausmann

unread,

Sep 4, 2013, 8:55:26 AM9/4/13

to itksna...@googlegroups.com, Paul Yushkevich

Hi Paul,

Thanks for Your reply.
On 03/09/13 16:38, Paul Yushkevich wrote:

> Do the linux versions crash when segmenting very large images (what size?) or
> any size images?

The crashes did not seem to depend on the size of the loaded image. We only ran
out of RAM on the windows machines with images > 600GB.

> The case when the bubbles don't grow, does that occur only when the bubbles
> are small or for large bubbles (>10 voxels across) too?

Also for large bubbles (e.g. 60 voxel) and for any kind of parameter combination
we tried.

I just managed to compile 2.4.2 from git with itk-3.20.1 (needed to add
ITKIOReview to the main CMakeLists.txt) and vtk-5.10 which seems to run nicely,
no crashes so far and the snake-tool uses multiple cores. I think we can live
with that for now.
However it would be nice to have itksnap compile with itk>=4.3. Perhaps that
would already solve the bubble problem. Is there any other reason except the
changes of the API that itk>=4.3 is not yet supported?

Many thanks for Your help
Roman

> Thanks! Paul
>
>
> On Tue, Sep 3, 2013 at 8:08 AM, Dr. Roman Grothausmann
> <grothausm...@mh-hannover.de

> <mailto:grothausm...@mh-hannover.de>> wrote:
>
> Dear mailing list members,
>
>
> We've been using itksnap (2.2.0 and 2.4.0) under windows for some time now
> and it crashed very rarely. Now since we got bigger dataset that we want to
> segment with the snake tool we run out of memory. Therefore we want to use
> itksnap on a server running linux with lots of RAM but there both the
> pre-compiled versions of itksnap (2.2.0, 2.4.0, 2.5.0-alpha) and also
> self-build ones (2.4.0, 2.4.2 or qtsnap) crash within a few minutes of usage
> and/or the snake tool runs very quickly but does not change the active
> contour at all. What would be the best way to debug these problems under
> linux? Building itksnap from source only worked with itk-4.2.1 however
> itk-4.2.1 seems not to be multi-threaded and the snake tool often does not
> evolve. I tried also to link against itk-4.3 and itk-4.4 (which again are
> able to use multiple threads) but it seems itksnap is not yet adjusted to
> the changes of the API. Is it planned to adjust the source of itksnap to
> comply to itk > 4.2.1 in the near future?
>
> Any help or hints are very much appreciated Roman -- Dr. Roman Grothausmann
>
> Tomographie und Digitale Bildverarbeitung Tomography and Digital Image
> Analysis
>

> Institut f�r Funktionelle und Angewandte Anatomie, OE 4120 Medizinische

> Hochschule Hannover Carl-Neuberg-Str. 1 D-30625 Hannover
>

> Tel. +49 511 532-9574 <tel:%2B49%20511%20532-9574>

>
> -- You received this message because you are subscribed to the Google Groups
> "itksnap-users" group. To unsubscribe from this group and stop receiving

> emails from it, send an email to itksnap-users+unsubscribe@__googlegroups.com
> <mailto:itksnap-users%2Bunsu...@googlegroups.com>. To post to this

> group, send email to itksna...@googlegroups.com

> <mailto:itksna...@googlegroups.com>__. Visit this group at
> http://groups.google.com/__group/itksnap-users
> <http://groups.google.com/group/itksnap-users>. For more options, visit
> https://groups.google.com/__groups/opt_out
> <https://groups.google.com/groups/opt_out>.

>
>
>
>
> -- Paul A. Yushkevich, Ph.D. Associate Professor Penn Image Computing and
> Science Laboratory Department of Radiology University of Pennsylvania
>

> -- You received this message because you are subscribed to the Google Groups
> "itksnap-users" group. To unsubscribe from this group and stop receiving

> emails from it, send an email to itksnap-user...@googlegroups.com.

> To post to this group, send email to itksna...@googlegroups.com. Visit
> this group at http://groups.google.com/group/itksnap-users. For more
> options, visit https://groups.google.com/groups/opt_out.

--

Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f�r Funktionelle und Angewandte Anatomie, OE 4120

Paul Yushkevich

unread,

Sep 8, 2013, 6:51:01 AM9/8/13

to Dr. Roman Grothausmann, itksna...@googlegroups.com

Hi Roman,

I am sorry, I did not check the fixed I made into Git, because I didn't want to switch to ITK 4.4 yet for all my nightly builds (that's a big effort). I am not sure that we gain anything with 4.4, as the bubble bug is still there.

Could you explain the problem you are seeing with running in parallel on multiple cores with 4.2? On my mac, ITK-SNAP 2.4 compiled with ITK 4.2 does utilize multiple cores.

Thanks!
Paul

On Fri, Sep 6, 2013 at 4:26 AM, Dr. Roman Grothausmann <grothausm...@mh-hannover.de> wrote:

Hi Paul,

Many thanks for looking into this.

On 04/09/13 16:28, Paul Yushkevich wrote:

I got SNAP to compile with ITK 4.4 last night, but the same problems persist.

That's great. Sadly my compilation still aborts with the errors below. That happens with both git chechouts (do I use the wrong ones?):
git clone http://git.code.sf.net/p/itk-snap/src itksnap-src
git clone http://git.code.sf.net/p/itk-snap/src -b qtsnap qtsnap_src

Any idea what could be wrong?

Thanks for Your help
Roman

PS: When I post to the list I always get two messages like this:
[Suspicious Attachm.] Transient Delivery Failure
Warning: c...@medfak.ni.ac.rs - User unknown!

______________________________________________________

[ 64%] Building CXX object CMakeFiles/itksnaplogic.dir/Logic/Common/SNAPRegistryIO.cxx.o
In file included from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:49:0,
from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40,
from /home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from /home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:53:9: error: ?GetImageDimension? is not a member of ?itk?
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:53:9: error: ?GetImageDimension? is not a member of ?itk?
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:53:45: error: template argument 2 is invalid
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:53:62: error: template argument 1 is invalid
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:54:7: error: ?GetImageDimension? is not a member of ?itk?
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:54:7: error: ?GetImageDimension? is not a member of ?itk?
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:54:43: error: wrong number of template arguments (3, should be 2)
In file included from /home/grothama/programme/qtsnap_src/Logic/Slicing/IntensityToColorLookupTableImageFilter.h:5:0,
from /home/grothama/programme/qtsnap_src/Logic/ImageWrapper/DisplayMappingPolicy.h:7,
from /home/grothama/programme/qtsnap_src/Logic/ImageWrapper/ImageWrapperTraits.h:8,
from /home/grothama/programme/qtsnap_src/Logic/Framework/GenericImageData.h:48,
from /home/grothama/programme/qtsnap_src/Logic/Framework/IRISImageData.h:38,
from /home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:39:
/opt/itk-4.4.2/include/ITK-4.4/itkImageToImageFilter.h:102:18: error: provided for ?template<class TInputImage, class TOutputImage> class itk::ImageToImageFilter?
In file included from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:49:0,
from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40,
from /home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from /home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:54:44: error: expected ?{? before ?::? token
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:54:60: error: expected initializer before ?>? token
In file included from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:111:0,
from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:49,
from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40,
from /home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from /home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.txx:40:33: error: invalid use of incomplete type ?class SNAPAdvectionFieldImageFilter<TInputImage, TOutputValueType>?
In file included from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:49:0,
from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40,
from /home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from /home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:48:7: error: declaration of ?class SNAPAdvectionFieldImageFilter<TInputImage, TOutputValueType>?
In file included from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:111:0,
from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:49,
from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40,
from /home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from /home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.txx:48:16: error: invalid use of incomplete type ?class SNAPAdvectionFieldImageFilter<TInputImage, TOutputValueType>?
In file included from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:49:0,
from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40,
from /home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from /home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:48:7: error: declaration of ?class SNAPAdvectionFieldImageFilter<TInputImage, TOutputValueType>?
In file included from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:111:0,
from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:49,
from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40,
from /home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from /home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.txx:94:51: error: invalid use of incomplete type ?class SNAPAdvectionFieldImageFilter<TInputImage, TOutputValueType>?
In file included from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:49:0,
from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40,
from /home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from /home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:48:7: error: declaration of ?class SNAPAdvectionFieldImageFilter<TInputImage, TOutputValueType>?
In file included from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40:0,
from /home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from /home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h: In instantiation of ?class SNAPLevelSetFunction<itk::Image<short int, 3u>, itk::Image<float, 3u> >?:
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:130:61: required from ?class SNAPLevelSetDriver<3u>?
/home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:197:24: required from here
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:332:41: error: invalid use of incomplete type ?class SNAPAdvectionFieldImageFilter<itk::Image<short int, 3u>, float>?
In file included from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:49:0,
from /home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40,
from /home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from /home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:48:7: error: declaration of ?class SNAPAdvectionFieldImageFilter<itk::Image<short int, 3u>, float>?
make[2]: *** [CMakeFiles/itksnaplogic.dir/Logic/Common/SNAPRegistryIO.cxx.o] Error 1
make[1]: *** [CMakeFiles/itksnaplogic.dir/all] Error 2
make: *** [all] Error 2

On Wed, Sep 4, 2013 at 8:55 AM, Dr. Roman Grothausmann

<grothausmann.roman@mh-hannover.de <mailto:grothausmann.roman@mh-hannover.de>>

wrote:

Hi Paul,

Thanks for Your reply.

On 03/09/13 16:38, Paul Yushkevich wrote:

Do the linux versions crash when segmenting very large images (what
size?) or
any size images?

The crashes did not seem to depend on the size of the loaded image. We only ran
out of RAM on the windows machines with images > 600GB.

The case when the bubbles don't grow, does that occur only when the bubbles
are small or for large bubbles (>10 voxels across) too?

Also for large bubbles (e.g. 60 voxel) and for any kind of parameter combination
we tried.

I just managed to compile 2.4.2 from git with itk-3.20.1 (needed to add
ITKIOReview to the main CMakeLists.txt) and vtk-5.10 which seems to run
nicely, no crashes so far and the snake-tool uses multiple cores. I think we
can live with that for now.
However it would be nice to have itksnap compile with itk>=4.3. Perhaps that
would already solve the bubble problem. Is there any other reason except the
changes of the API that itk>=4.3 is not yet supported?

Many thanks for Your help
Roman

Thanks! Paul

On Tue, Sep 3, 2013 at 8:08 AM, Dr. Roman Grothausmann

<grothausmann.roman@mh-__hannover.de
<mailto:grothausmann.roman@mh-hannover.de>
<mailto:grothausmann.roman@mh-__hannover.de

itksnap-users+unsubscribe@__go__oglegroups.com <http://googlegroups.com>
<mailto:itksnap-users%__2Bunsu...@googlegroups.com
<mailto:itksnap-users%252Bunsubscribe@googlegroups.com>__>. To post to this

group, send email to itksna...@googlegroups.com
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-- Paul A. Yushkevich, Ph.D. Associate Professor Penn Image Computing and
Science Laboratory Department of Radiology University of Pennsylvania

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Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574 <tel:%2B49%20511%20532-9574>

--

Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

--

Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574

Paul Yushkevich

unread,

Sep 16, 2013, 11:16:56 AM9/16/13

to Dr. Roman Grothausmann, itksna...@googlegroups.com

Roman,

Please try this patch file against the current git.

Thanks!
Paul

On Mon, Sep 16, 2013 at 11:03 AM, Dr. Roman Grothausmann <grothausm...@mh-hannover.de> wrote:

Hi Paul,

On 08/09/13 12:51, Paul Yushkevich wrote:

Hi Roman,

I am sorry, I did not check the fixed I made into Git, because I didn't want to
switch to ITK 4.4 yet for all my nightly builds (that's a big effort). I am not
sure that we gain anything with 4.4, as the bubble bug is still there.

Well, I would try to find the origin of that bug, but since so far itk 4.2.1 is the only ITK4 version I manage to compile itksnap with and itk-4.2.1 somehow does not work properly for me (tried nine times to have itk-4.2 use multiple cores, however 4.3 and 4.4 work perfectly) I'd first like to get itksnap to run with an itk4 using multiple cores before I start trying to find the origin of the bubble bug.
Is there any way I could get the changes You made to make itksnap compile with itk 4.4? Perhaps just a patch file via email?

Could you explain the problem you are seeing with running in parallel on
multiple cores with 4.2? On my mac, ITK-SNAP 2.4 compiled with ITK 4.2 does
utilize multiple cores.

I've no clue why my itk-4.2.1 does not use multiple cores, however itk-4.3 and 4.4 work well, so I'd like to just stick to those.

Kind regards,
Roman

On Fri, Sep 6, 2013 at 4:26 AM, Dr. Roman Grothausmann

<grothausmann.roman@mh-hannover.de <mailto:grothausmann.roman@mh-hannover.de>>
wrote:

Hi Paul,

Many thanks for looking into this.

On 04/09/13 16:28, Paul Yushkevich wrote:

I got SNAP to compile with ITK 4.4 last night, but the same problems
persist.

That's great. Sadly my compilation still aborts with the errors below. That
happens with both git chechouts (do I use the wrong ones?):

git clone http://git.code.sf.net/p/itk-__snap/src
<http://git.code.sf.net/p/itk-snap/src> itksnap-src
git clone http://git.code.sf.net/p/itk-__snap/src

<http://git.code.sf.net/p/itk-snap/src> -b qtsnap qtsnap_src

Any idea what could be wrong?

Thanks for Your help
Roman

PS: When I post to the list I always get two messages like this:
[Suspicious Attachm.] Transient Delivery Failure

Warning: c...@medfak.ni.ac.rs <mailto:c...@medfak.ni.ac.rs> - User unknown!

________________________________________________________

[ 64%] Building CXX object
CMakeFiles/itksnaplogic.dir/__Logic/Common/SNAPRegistryIO.__cxx.o
In file included from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:49:0,
from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40,
from
/home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
from
/home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:53:9:

error: ?GetImageDimension? is not a member of ?itk?

/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:53:9:

error: ?GetImageDimension? is not a member of ?itk?

/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:53:45:

error: template argument 2 is invalid

/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:53:62:

error: template argument 1 is invalid

/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:54:7:

error: ?GetImageDimension? is not a member of ?itk?

/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:54:7:

error: ?GetImageDimension? is not a member of ?itk?

/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:54:43:

error: wrong number of template arguments (3, should be 2)
In file included from

/home/grothama/programme/__qtsnap_src/Logic/Slicing/__IntensityToColorLookupTableIma__geFilter.h:5:0,
from
/home/grothama/programme/__qtsnap_src/Logic/ImageWrapper/__DisplayMappingPolicy.h:7,
from
/home/grothama/programme/__qtsnap_src/Logic/ImageWrapper/__ImageWrapperTraits.h:8,
from
/home/grothama/programme/__qtsnap_src/Logic/Framework/__GenericImageData.h:48,
from
/home/grothama/programme/__qtsnap_src/Logic/Framework/__IRISImageData.h:38,
from
/home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:39:
/opt/itk-4.4.2/include/ITK-4.__4/itkImageToImageFilter.h:102:__18: error:

provided for ?template<class TInputImage, class TOutputImage> class
itk::ImageToImageFilter?
In file included from

/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:49:0,
from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40,
from
/home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
from
/home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:54:44:

error: expected ?{? before ?::? token

/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:54:60:

error: expected initializer before ?>? token
In file included from

/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:111:0,
from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:49,
from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40,
from
/home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
from
/home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__txx:40:33:

error: invalid use of incomplete type ?class

SNAPAdvectionFieldImageFilter<__TInputImage, TOutputValueType>?
In file included from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:49:0,
from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40,
from
/home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
from
/home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:48:7:
error: declaration of ?class SNAPAdvectionFieldImageFilter<__TInputImage,

TOutputValueType>?
In file included from

/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:111:0,
from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:49,
from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40,
from
/home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
from
/home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__txx:48:16:

error: invalid use of incomplete type ?class

SNAPAdvectionFieldImageFilter<__TInputImage, TOutputValueType>?
In file included from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:49:0,
from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40,
from
/home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
from
/home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:48:7:
error: declaration of ?class SNAPAdvectionFieldImageFilter<__TInputImage,

TOutputValueType>?
In file included from

/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:111:0,
from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:49,
from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40,
from
/home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
from
/home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__txx:94:51:

error: invalid use of incomplete type ?class

SNAPAdvectionFieldImageFilter<__TInputImage, TOutputValueType>?
In file included from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:49:0,
from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40,
from
/home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
from
/home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:48:7:
error: declaration of ?class SNAPAdvectionFieldImageFilter<__TInputImage,

TOutputValueType>?
In file included from

/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40:0,
from
/home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
from
/home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:
In instantiation of ?class SNAPLevelSetFunction<itk::__Image<short int, 3u>,

itk::Image<float, 3u> >?:

/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:130:61:

required from ?class SNAPLevelSetDriver<3u>?

/home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:197:24:
required from here
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:332:41:

error: invalid use of incomplete type ?class

SNAPAdvectionFieldImageFilter<__itk::Image<short int, 3u>, float>?
In file included from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:49:0,
from
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40,
from
/home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
from
/home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:
/home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:48:7:
error: declaration of ?class
SNAPAdvectionFieldImageFilter<__itk::Image<short int, 3u>, float>?
make[2]: ***
[CMakeFiles/itksnaplogic.dir/__Logic/Common/SNAPRegistryIO.__cxx.o] Error 1
make[1]: *** [CMakeFiles/itksnaplogic.dir/__all] Error 2

make: *** [all] Error 2

On Wed, Sep 4, 2013 at 8:55 AM, Dr. Roman Grothausmann

<grothausmann.roman@mh-____hannover.de
<mailto:grothausmann.roman@mh-__hannover.de>
<mailto:grothausmann.roman@mh-__hannover.de
<mailto:grothausmann.roman@mh-hannover.de>>
<mailto:grothausmann.roman@mh-____hannover.de
<mailto:grothausmann.roman@mh-__hannover.de>

itksnap-users+unsubscribe@__go____oglegroups.com
<http://go__oglegroups.com> <http://googlegroups.com>
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<mailto:itksnap-users%__252Bunsubscribe@googlegroups.__com
<mailto:itksnap-users%25252Bunsubscribe@googlegroups.com>>__>. To post

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<mailto:itksnap-users@googlegroups.com>
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<mailto:itksnap-users@>__google__groups.com <http://googlegroups.com>

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<mailto:itksnap-users@googlegroups.com>>>__. Visit this group at

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<http://groups.google.com/__group/itksnap-users>
<http://groups.google.com/__group/itksnap-users
<http://groups.google.com/group/itksnap-users>>>. For more options, visit

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<https://groups.google.com/____groups/opt_out>

Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574 <tel:%2B49%20511%20532-9574>
<tel:%2B49%20511%20532-9574>

--

patch_for_roman

Dr. Roman Grothausmann

unread,

Sep 16, 2013, 11:03:51 AM9/16/13

to Paul Yushkevich, itksna...@googlegroups.com

Hi Paul,

On 08/09/13 12:51, Paul Yushkevich wrote:

> Hi Roman,
>
> I am sorry, I did not check the fixed I made into Git, because I didn't want to
> switch to ITK 4.4 yet for all my nightly builds (that's a big effort). I am not
> sure that we gain anything with 4.4, as the bubble bug is still there.

Well, I would try to find the origin of that bug, but since so far itk 4.2.1 is
the only ITK4 version I manage to compile itksnap with and itk-4.2.1 somehow
does not work properly for me (tried nine times to have itk-4.2 use multiple
cores, however 4.3 and 4.4 work perfectly) I'd first like to get itksnap to run
with an itk4 using multiple cores before I start trying to find the origin of
the bubble bug.
Is there any way I could get the changes You made to make itksnap compile with
itk 4.4? Perhaps just a patch file via email?

>

> Could you explain the problem you are seeing with running in parallel on
> multiple cores with 4.2? On my mac, ITK-SNAP 2.4 compiled with ITK 4.2 does
> utilize multiple cores.

I've no clue why my itk-4.2.1 does not use multiple cores, however itk-4.3 and
4.4 work well, so I'd like to just stick to those.

Kind regards,
Roman

> On Fri, Sep 6, 2013 at 4:26 AM, Dr. Roman Grothausmann

> <grothausm...@mh-hannover.de <mailto:grothausm...@mh-hannover.de>>

> wrote:
>
> Hi Paul,
>
>
> Many thanks for looking into this.
>
> On 04/09/13 16:28, Paul Yushkevich wrote:
>
> I got SNAP to compile with ITK 4.4 last night, but the same problems
> persist.
>
>
> That's great. Sadly my compilation still aborts with the errors below. That
> happens with both git chechouts (do I use the wrong ones?):

> git clone http://git.code.sf.net/p/itk-__snap/src
> <http://git.code.sf.net/p/itk-snap/src> itksnap-src
> git clone http://git.code.sf.net/p/itk-__snap/src

> <http://git.code.sf.net/p/itk-snap/src> -b qtsnap qtsnap_src
>
> Any idea what could be wrong?
>
> Thanks for Your help
> Roman
>
> PS: When I post to the list I always get two messages like this:
> [Suspicious Attachm.] Transient Delivery Failure

> Warning: c...@medfak.ni.ac.rs <mailto:c...@medfak.ni.ac.rs> - User unknown!
>
> ________________________________________________________
>
> [ 64%] Building CXX object
> CMakeFiles/itksnaplogic.dir/__Logic/Common/SNAPRegistryIO.__cxx.o
> In file included from
> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:49:0,
> from
> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40,
> from
> /home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
> from
> /home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:53:9:

> error: ?GetImageDimension? is not a member of ?itk?

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:53:9:

> error: ?GetImageDimension? is not a member of ?itk?

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:53:45:

> error: template argument 2 is invalid

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:53:62:

> error: template argument 1 is invalid

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:54:7:

> error: ?GetImageDimension? is not a member of ?itk?

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:54:7:

> error: ?GetImageDimension? is not a member of ?itk?

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:54:43:

> error: wrong number of template arguments (3, should be 2)
> In file included from

> /home/grothama/programme/__qtsnap_src/Logic/Slicing/__IntensityToColorLookupTableIma__geFilter.h:5:0,
> from
> /home/grothama/programme/__qtsnap_src/Logic/ImageWrapper/__DisplayMappingPolicy.h:7,
> from
> /home/grothama/programme/__qtsnap_src/Logic/ImageWrapper/__ImageWrapperTraits.h:8,
> from
> /home/grothama/programme/__qtsnap_src/Logic/Framework/__GenericImageData.h:48,
> from
> /home/grothama/programme/__qtsnap_src/Logic/Framework/__IRISImageData.h:38,
> from
> /home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:39:

> /opt/itk-4.4.2/include/ITK-4.__4/itkImageToImageFilter.h:102:__18: error:

> provided for ?template<class TInputImage, class TOutputImage> class
> itk::ImageToImageFilter?
> In file included from

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:49:0,
> from
> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40,
> from
> /home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
> from
> /home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:54:44:

> error: expected ?{? before ?::? token

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:54:60:

> error: expected initializer before ?>? token
> In file included from

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:111:0,
> from
> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:49,
> from
> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40,
> from
> /home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
> from
> /home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__txx:40:33:

> error: invalid use of incomplete type ?class

> SNAPAdvectionFieldImageFilter<__TInputImage, TOutputValueType>?
> In file included from

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:48:7:
> error: declaration of ?class SNAPAdvectionFieldImageFilter<__TInputImage,

> TOutputValueType>?
> In file included from

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__txx:48:16:

> error: invalid use of incomplete type ?class

> SNAPAdvectionFieldImageFilter<__TInputImage, TOutputValueType>?
> In file included from

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:48:7:
> error: declaration of ?class SNAPAdvectionFieldImageFilter<__TInputImage,

> TOutputValueType>?
> In file included from

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__txx:94:51:

> error: invalid use of incomplete type ?class

> SNAPAdvectionFieldImageFilter<__TInputImage, TOutputValueType>?
> In file included from

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:48:7:
> error: declaration of ?class SNAPAdvectionFieldImageFilter<__TInputImage,

> TOutputValueType>?
> In file included from

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:40:0,
> from
> /home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:48,
> from
> /home/grothama/programme/__qtsnap_src/Logic/Common/__SNAPRegistryIO.cxx:40:
> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:

> In instantiation of ?class SNAPLevelSetFunction<itk::__Image<short int, 3u>,

> itk::Image<float, 3u> >?:

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetDriver.h:130:61:

> required from ?class SNAPLevelSetDriver<3u>?

> /home/grothama/programme/__qtsnap_src/Logic/Framework/__SNAPImageData.h:197:24:
> required from here
> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPLevelSetFunction.h:332:41:

> error: invalid use of incomplete type ?class

> SNAPAdvectionFieldImageFilter<__itk::Image<short int, 3u>, float>?
> In file included from

> /home/grothama/programme/__qtsnap_src/Logic/LevelSet/__SNAPAdvectionFieldImageFilter.__h:48:7:
> error: declaration of ?class
> SNAPAdvectionFieldImageFilter<__itk::Image<short int, 3u>, float>?
> make[2]: ***
> [CMakeFiles/itksnaplogic.dir/__Logic/Common/SNAPRegistryIO.__cxx.o] Error 1
> make[1]: *** [CMakeFiles/itksnaplogic.dir/__all] Error 2

> make: *** [all] Error 2
>
>
>
> On Wed, Sep 4, 2013 at 8:55 AM, Dr. Roman Grothausmann

> <grothausmann.roman@mh-__hannover.de
> <mailto:grothausm...@mh-hannover.de>
> <mailto:grothausmann.roman@mh-__hannover.de
> <mailto:grothausm...@mh-hannover.de>>>

> <grothausmann.roman@mh-____hannover.de
> <mailto:grothausmann.roman@mh-__hannover.de>
> <mailto:grothausmann.roman@mh-__hannover.de

> <mailto:grothausm...@mh-hannover.de>>

> <mailto:grothausmann.roman@mh-____hannover.de
> <mailto:grothausmann.roman@mh-__hannover.de>
>
> <mailto:grothausmann.roman@mh-__hannover.de

> Institut f�r Funktionelle und Angewandte Anatomie, OE 4120

> Medizinische
> Hochschule Hannover Carl-Neuberg-Str. 1 D-30625 Hannover
>
> Tel. +49 511 532-9574 <tel:%2B49%20511%20532-9574>
> <tel:%2B49%20511%20532-9574>
> <tel:%2B49%20511%20532-9574>
>
>
> -- You received this message because you are subscribed to the
> Google Groups
> "itksnap-users" group. To unsubscribe from this group and
> stop receiving
> emails from it, send an email to

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> <mailto:itksnap-users%__252Bunsubscribe@googlegroups.__com
> <mailto:itksnap-users%25252Bun...@googlegroups.com>>__>. To post

> to this
>
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> group, send email to itksna...@googlegroups.com

> <mailto:itksna...@googlegroups.com>
> <mailto:itksnap-users@__googlegroups.com
> <mailto:itksna...@googlegroups.com>>

> <mailto:itksnap-users@
> <mailto:itksnap-users@>__google__groups.com <http://googlegroups.com>
>
> <mailto:itksnap-users@__googlegroups.com

> <mailto:itksna...@googlegroups.com>>>__. Visit this group at
> http://groups.google.com/______group/itksnap-users
> <http://groups.google.com/____group/itksnap-users>

> <http://groups.google.com/____group/itksnap-users
> <http://groups.google.com/__group/itksnap-users>>
>
> <http://groups.google.com/____group/itksnap-users
> <http://groups.google.com/__group/itksnap-users>
> <http://groups.google.com/__group/itksnap-users
> <http://groups.google.com/group/itksnap-users>>>. For more options, visit

> https://groups.google.com/______groups/opt_out
> <https://groups.google.com/____groups/opt_out>

> <https://groups.google.com/____groups/opt_out
> <https://groups.google.com/__groups/opt_out>>
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> <https://groups.google.com/____groups/opt_out
> <https://groups.google.com/__groups/opt_out>
> <https://groups.google.com/__groups/opt_out
> <https://groups.google.com/groups/opt_out>>>.
>
>
>
>
>
> -- Paul A. Yushkevich, Ph.D. Associate Professor Penn Image
> Computing and
> Science Laboratory Department of Radiology University of
> Pennsylvania
>
> -- You received this message because you are subscribed to the
> Google Groups
> "itksnap-users" group. To unsubscribe from this group and
> stop receiving
> emails from it, send an email to

> itksnap-users+unsubscribe@__go__oglegroups.com
> <http://googlegroups.com>
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> <mailto:itksnap-users%252Buns...@googlegroups.com>__>.

> To post to this group, send email to

> itksna...@googlegroups.com <mailto:itksna...@googlegroups.com>
> <mailto:itksnap-users@__googlegroups.com
> <mailto:itksna...@googlegroups.com>>__. Visit

> this group at http://groups.google.com/____group/itksnap-users
> <http://groups.google.com/__group/itksnap-users>
> <http://groups.google.com/__group/itksnap-users
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> <https://groups.google.com/__groups/opt_out
> <https://groups.google.com/groups/opt_out>>.
>
>
> --

> Dr. Roman Grothausmann
>
> Tomographie und Digitale Bildverarbeitung
> Tomography and Digital Image Analysis
>

> Institut f�r Funktionelle und Angewandte Anatomie, OE 4120

> Medizinische Hochschule Hannover
> Carl-Neuberg-Str. 1
> D-30625 Hannover
>
> Tel. +49 511 532-9574 <tel:%2B49%20511%20532-9574>
> <tel:%2B49%20511%20532-9574>
>
>
>
>
> --

> Paul A. Yushkevich, Ph.D.
> Associate Professor
> Penn Image Computing and Science Laboratory
> Department of Radiology
> University of Pennsylvania
>
>
> --
> Dr. Roman Grothausmann
>
> Tomographie und Digitale Bildverarbeitung
> Tomography and Digital Image Analysis
>

> Institut f�r Funktionelle und Angewandte Anatomie, OE 4120

> Medizinische Hochschule Hannover
> Carl-Neuberg-Str. 1
> D-30625 Hannover
>
> Tel. +49 511 532-9574 <tel:%2B49%20511%20532-9574>
>
>
>
>
> --
> Paul A. Yushkevich, Ph.D.
> Associate Professor
> Penn Image Computing and Science Laboratory
> Department of Radiology
> University of Pennsylvania

--
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f�r Funktionelle und Angewandte Anatomie, OE 4120

Dr. Roman Grothausmann

unread,

Sep 6, 2013, 4:26:26 AM9/6/13

to Paul Yushkevich, itksna...@googlegroups.com

Hi Paul,

Many thanks for looking into this.
On 04/09/13 16:28, Paul Yushkevich wrote:

> I got SNAP to compile with ITK 4.4 last night, but the same problems persist.

That's great. Sadly my compilation still aborts with the errors below. That
happens with both git chechouts (do I use the wrong ones?):

git clone http://git.code.sf.net/p/itk-snap/src itksnap-src
git clone http://git.code.sf.net/p/itk-snap/src -b qtsnap qtsnap_src

Any idea what could be wrong?

Thanks for Your help
Roman

PS: When I post to the list I always get two messages like this:
[Suspicious Attachm.] Transient Delivery Failure

Warning: c...@medfak.ni.ac.rs - User unknown!

______________________________________________________

[ 64%] Building CXX object
CMakeFiles/itksnaplogic.dir/Logic/Common/SNAPRegistryIO.cxx.o
In file included from
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:49:0,
from
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40,
from
/home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from
/home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:53:9:

error: ?GetImageDimension? is not a member of ?itk?

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:53:9:

error: ?GetImageDimension? is not a member of ?itk?

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:53:45:

error: template argument 2 is invalid

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:53:62:

error: template argument 1 is invalid

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:54:7:

error: ?GetImageDimension? is not a member of ?itk?

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:54:7:

error: ?GetImageDimension? is not a member of ?itk?

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:54:43:

error: wrong number of template arguments (3, should be 2)
In file included from

/home/grothama/programme/qtsnap_src/Logic/Slicing/IntensityToColorLookupTableImageFilter.h:5:0,
from
/home/grothama/programme/qtsnap_src/Logic/ImageWrapper/DisplayMappingPolicy.h:7,
from
/home/grothama/programme/qtsnap_src/Logic/ImageWrapper/ImageWrapperTraits.h:8,
from
/home/grothama/programme/qtsnap_src/Logic/Framework/GenericImageData.h:48,
from
/home/grothama/programme/qtsnap_src/Logic/Framework/IRISImageData.h:38,
from
/home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:39:

/opt/itk-4.4.2/include/ITK-4.4/itkImageToImageFilter.h:102:18: error: provided

for ?template<class TInputImage, class TOutputImage> class itk::ImageToImageFilter?
In file included from

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:49:0,
from
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40,
from
/home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from
/home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:54:44:

error: expected ?{? before ?::? token

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:54:60:

error: expected initializer before ?>? token
In file included from

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:111:0,
from
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:49,
from
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40,
from
/home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from
/home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.txx:40:33:

error: invalid use of incomplete type ?class

SNAPAdvectionFieldImageFilter<TInputImage, TOutputValueType>?
In file included from

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:48:7:
error: declaration of ?class SNAPAdvectionFieldImageFilter<TInputImage,

TOutputValueType>?
In file included from

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.txx:48:16:

error: invalid use of incomplete type ?class

SNAPAdvectionFieldImageFilter<TInputImage, TOutputValueType>?
In file included from

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:48:7:
error: declaration of ?class SNAPAdvectionFieldImageFilter<TInputImage,

TOutputValueType>?
In file included from

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.txx:94:51:

error: invalid use of incomplete type ?class

SNAPAdvectionFieldImageFilter<TInputImage, TOutputValueType>?
In file included from

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:48:7:
error: declaration of ?class SNAPAdvectionFieldImageFilter<TInputImage,

TOutputValueType>?
In file included from

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:40:0,
from
/home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:48,
from
/home/grothama/programme/qtsnap_src/Logic/Common/SNAPRegistryIO.cxx:40:

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h: In
instantiation of ?class SNAPLevelSetFunction<itk::Image<short int, 3u>,

itk::Image<float, 3u> >?:

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetDriver.h:130:61:

required from ?class SNAPLevelSetDriver<3u>?

/home/grothama/programme/qtsnap_src/Logic/Framework/SNAPImageData.h:197:24:
required from here
/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPLevelSetFunction.h:332:41: error:

invalid use of incomplete type ?class

SNAPAdvectionFieldImageFilter<itk::Image<short int, 3u>, float>?
In file included from

/home/grothama/programme/qtsnap_src/Logic/LevelSet/SNAPAdvectionFieldImageFilter.h:48:7:
error: declaration of ?class SNAPAdvectionFieldImageFilter<itk::Image<short int,
3u>, float>?
make[2]: *** [CMakeFiles/itksnaplogic.dir/Logic/Common/SNAPRegistryIO.cxx.o] Error 1
make[1]: *** [CMakeFiles/itksnaplogic.dir/all] Error 2

make: *** [all] Error 2

>

> On Wed, Sep 4, 2013 at 8:55 AM, Dr. Roman Grothausmann

> <grothausm...@mh-hannover.de <mailto:grothausm...@mh-hannover.de>>

> wrote:
>
> Hi Paul,
>
>
> Thanks for Your reply.
>
> On 03/09/13 16:38, Paul Yushkevich wrote:
>
> Do the linux versions crash when segmenting very large images (what
> size?) or
> any size images?
>
>
> The crashes did not seem to depend on the size of the loaded image. We only ran
> out of RAM on the windows machines with images > 600GB.
>
>
> The case when the bubbles don't grow, does that occur only when the bubbles
> are small or for large bubbles (>10 voxels across) too?
>
>
> Also for large bubbles (e.g. 60 voxel) and for any kind of parameter combination
> we tried.
>
> I just managed to compile 2.4.2 from git with itk-3.20.1 (needed to add
> ITKIOReview to the main CMakeLists.txt) and vtk-5.10 which seems to run
> nicely, no crashes so far and the snake-tool uses multiple cores. I think we
> can live with that for now.
> However it would be nice to have itksnap compile with itk>=4.3. Perhaps that
> would already solve the bubble problem. Is there any other reason except the
> changes of the API that itk>=4.3 is not yet supported?
>
> Many thanks for Your help
> Roman
>
> Thanks! Paul
>
>
> On Tue, Sep 3, 2013 at 8:08 AM, Dr. Roman Grothausmann

> <grothausmann.roman@mh-__hannover.de
> <mailto:grothausm...@mh-hannover.de>
> <mailto:grothausmann.roman@mh-__hannover.de

> <mailto:grothausm...@mh-hannover.de>>> wrote:
>
> Dear mailing list members,
>
>
> We've been using itksnap (2.2.0 and 2.4.0) under windows for some time now
> and it crashed very rarely. Now since we got bigger dataset that we want to
> segment with the snake tool we run out of memory. Therefore we want to use
> itksnap on a server running linux with lots of RAM but there both the
> pre-compiled versions of itksnap (2.2.0, 2.4.0, 2.5.0-alpha) and also
> self-build ones (2.4.0, 2.4.2 or qtsnap) crash within a few minutes of usage
> and/or the snake tool runs very quickly but does not change the active
> contour at all. What would be the best way to debug these problems under
> linux? Building itksnap from source only worked with itk-4.2.1 however
> itk-4.2.1 seems not to be multi-threaded and the snake tool often does not
> evolve. I tried also to link against itk-4.3 and itk-4.4 (which again are
> able to use multiple threads) but it seems itksnap is not yet adjusted to
> the changes of the API. Is it planned to adjust the source of itksnap to
> comply to itk > 4.2.1 in the near future?
>
> Any help or hints are very much appreciated Roman -- Dr. Roman Grothausmann
>
> Tomographie und Digitale Bildverarbeitung Tomography and Digital Image
> Analysis
>

> Institut f�r Funktionelle und Angewandte Anatomie, OE 4120 Medizinische

> Hochschule Hannover Carl-Neuberg-Str. 1 D-30625 Hannover
>
> Tel. +49 511 532-9574 <tel:%2B49%20511%20532-9574>
> <tel:%2B49%20511%20532-9574>
>
>
> -- You received this message because you are subscribed to the Google Groups
> "itksnap-users" group. To unsubscribe from this group and stop receiving
> emails from it, send an email to

> itksnap-users+unsubscribe@__go__oglegroups.com <http://googlegroups.com>
> <mailto:itksnap-users%__2Buns...@googlegroups.com

> <mailto:itksnap-users%252Buns...@googlegroups.com>__>. To post to this

>
> group, send email to itksna...@googlegroups.com

> <mailto:itksna...@googlegroups.com>
> <mailto:itksnap-users@__googlegroups.com
> <mailto:itksna...@googlegroups.com>>__. Visit this group at
> http://groups.google.com/____group/itksnap-users
> <http://groups.google.com/__group/itksnap-users>

> <http://groups.google.com/__group/itksnap-users
> <http://groups.google.com/group/itksnap-users>>. For more options, visit

> https://groups.google.com/____groups/opt_out
> <https://groups.google.com/__groups/opt_out>

> <https://groups.google.com/__groups/opt_out
> <https://groups.google.com/groups/opt_out>>.
>
>
>
>
>
> -- Paul A. Yushkevich, Ph.D. Associate Professor Penn Image Computing and
> Science Laboratory Department of Radiology University of Pennsylvania
>
> -- You received this message because you are subscribed to the Google Groups
> "itksnap-users" group. To unsubscribe from this group and stop receiving
> emails from it, send an email to

> itksnap-users+unsubscribe@__googlegroups.com
> <mailto:itksnap-users%2Bunsu...@googlegroups.com>.
> To post to this group, send email to itksna...@googlegroups.com

> <mailto:itksna...@googlegroups.com>__. Visit

> this group at http://groups.google.com/__group/itksnap-users
> <http://groups.google.com/group/itksnap-users>. For more
> options, visit https://groups.google.com/__groups/opt_out
> <https://groups.google.com/groups/opt_out>.
>
>
> --

> Dr. Roman Grothausmann
>
> Tomographie und Digitale Bildverarbeitung
> Tomography and Digital Image Analysis
>

> Institut f�r Funktionelle und Angewandte Anatomie, OE 4120

> Medizinische Hochschule Hannover
> Carl-Neuberg-Str. 1
> D-30625 Hannover
>
> Tel. +49 511 532-9574 <tel:%2B49%20511%20532-9574>
>
>
>
>
> --

> Paul A. Yushkevich, Ph.D.
> Associate Professor
> Penn Image Computing and Science Laboratory
> Department of Radiology
> University of Pennsylvania

--

Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f�r Funktionelle und Angewandte Anatomie, OE 4120

Dr. Roman Grothausmann

unread,

Sep 17, 2013, 10:09:57 AM9/17/13

to Paul Yushkevich, itksna...@googlegroups.com

Many thanks Paul for the patch. It compiles fine with itk-4.4.2 now and itsnap
runs stable and uses multiple cores (e.g. with the levelset segmentation tool).
The problem with some bubbles not expanding still remains (as expected). I'll
have a look if I can find something. To rule out that it is a itksnap problem
but an itk bug, I wonder if the same problem has been observed when convert3d
was used with the same speed-image itksnap generates and the initial segment one
gets from the added bubbles?

Thanks again for the patch Paul.
Roman

PS: Before I clumsily start adjusting files of convert3d according to Your
itksnap-patch to support the itk 4.4 API, I wonder if You have already done any
adjustments on convert3d to support 4.4? If so would You send me a patch as well?

On 16/09/13 17:16, Paul Yushkevich wrote:
> Roman,
>
> Please try this patch file against the current git.
>
> Thanks!
> Paul
>

--
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f�r Funktionelle und Angewandte Anatomie, OE 4120

Paul Yushkevich

unread,

Sep 17, 2013, 10:17:06 AM9/17/13

to Dr. Roman Grothausmann, itksna...@googlegroups.com

Hi Roman,

I don't have a patch because I haven't tried building convert3d against ITK 4.4 yet, but I do observe similar behavior when I use C3D.

Thanks!

Paul

On Tue, Sep 17, 2013 at 10:09 AM, Dr. Roman Grothausmann <grothausm...@mh-hannover.de> wrote:

Many thanks Paul for the patch. It compiles fine with itk-4.4.2 now and itsnap runs stable and uses multiple cores (e.g. with the levelset segmentation tool). The problem with some bubbles not expanding still remains (as expected). I'll have a look if I can find something. To rule out that it is a itksnap problem but an itk bug, I wonder if the same problem has been observed when convert3d was used with the same speed-image itksnap generates and the initial segment one gets from the added bubbles?

Thanks again for the patch Paul.
Roman

PS: Before I clumsily start adjusting files of convert3d according to Your itksnap-patch to support the itk 4.4 API, I wonder if You have already done any adjustments on convert3d to support 4.4? If so would You send me a patch as well?

On 16/09/13 17:16, Paul Yushkevich wrote:

Roman,

Please try this patch file against the current git.

Thanks!
Paul

--
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut für Funktionelle und Angewandte Anatomie, OE 4120

Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574

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