[Insight-users] help
Clark Teresa (North Cumbria Acute Hospitals NHS Trust)
teresa.clark at nhs.net
Mon May 18 11:40:31 EDT 2009
Please unsubscribe me. I have tried several methods, none of which has worked!
Teresa
Teresa Clark
Senior Physicist
Medical Physics Department (Radiotherapy section)
Cumberland Infirmary
Newtown Road
Carlisle
CA2 7HY
Tel: 07701018450
Email: teresa.clark at nhs.net
or: teresa.clark at ncumbria-acute.nhs.uk
-----Original Message-----
From: insight-users-bounces at itk.org [mailto:insight-users-bounces at itk.org] On Behalf Of insight-users-request at itk.org
Sent: 18 May 2009 15:04
To: insight-users at itk.org
Subject: Insight-users Digest, Vol 61, Issue 63
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Today's Topics:
1. Re: PET Images (x0_y0_0)
2. Writing Resampled Images With New Orientation (Kon Z)
3. Re: Writing Resampled Images With New Orientation (Andreas Schuh)
4. Writing mesh to Metafile (Matilde Gonzalez Preciado)
5. unsubscribe
(Clark Teresa (North Cumbria Acute Hospitals NHS Trust))
----------------------------------------------------------------------
Message: 1
Date: Mon, 18 May 2009 19:18:05 +0800 (CST)
From: x0_y0_0 <x0_y0_0 at 126.com>
Subject: Re: [Insight-users] PET Images
To: "JOHN ATKINSON" <johnimager at gmail.com>, itk
<insight-users at itk.org>
Message-ID:
<19888064.620691242645485162.JavaMail.coremail at bj126app21.126.com>
Content-Type: text/plain; charset="gbk"
http://pubimage.hcuge.ch:8080/
?2009-05-17?14:14:29?"JOHN?ATKINSON"?<johnimager at gmail.com>????
>Hi?All,
>
>
>I?wan?some?PET?images?for?volume?rendering?application.Can?some?one
>tell?me?the?link?from?which?I?can?download?PET?Images?preferably?DICOM
>or?analyze.Thanks?in?Advance
>
>
>
>Regards
>
>John
>_____________________________________
>Powered?by?www.kitware.com
>
>Visit?other?Kitware?open-source?projects?at
>http://www.kitware.com/opensource/opensource.html
>
>Please?keep?messages?on-topic?and?check?the?ITK?FAQ?at:?http://www.itk.org/Wiki/ITK_FAQ
>
>Follow?this?link?to?subscribe/unsubscribe:
>http://www.itk.org/mailman/listinfo/insight-users
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Message: 2
Date: Mon, 18 May 2009 13:01:15 +0100
From: Kon Z <mnkz at comp.leeds.ac.uk>
Subject: [Insight-users] Writing Resampled Images With New Orientation
To: insight-users at itk.org
Message-ID: <4A114E0B.7090900 at comp.leeds.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hello ALL,
When I use ResampleImageFilter to resample an 3D image with a new
direction matrix
resampler->SetOutputDirection(directionMatrix);
the filter output shows the specified orientation (with the values I
specify in the direction matrix):
Direction:
0.529919 0.46188 -0.711233
0 0.838671 0.544639
0.848048 -0.288615 0.444428
However, when I pass resample filter output to a writer connected to
GDCMImageIO, the saved volume has this orientation (the direction matrix
is transposed!):
Direction:
0.529919 0 0.848048
0.46188 0.838671 -0.288615
-0.711233 0.544639 0.444428
Am I doing something wrong? Or am I not doing something I'm supposed to
do with the image before passing it to the writer? Can someone please
explain it to me?
For the moment I use this workaround I found in the ITK Guide:
itk::EncapsulateMetaData<std::string>(
resampler->GetOutput()->GetMetaDataDictionary(),
"0020|0037", // Patient orientation tag.
directionStream.str().c_str());
where directionStream contains the correct string representation of the
directionMatrix.
Thanks.
Best regards,
Kon Z
------------------------------
Message: 3
Date: Mon, 18 May 2009 14:05:55 +0200
From: Andreas Schuh <andreas.schuh.84 at googlemail.com>
Subject: Re: [Insight-users] Writing Resampled Images With New
Orientation
To: Kon Z <mnkz at comp.leeds.ac.uk>
Cc: insight-users at itk.org
Message-ID: <4A114F23.8030203 at googlemail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Kon,
this actually is exactly what I reported yet as bug .. However,
unfortunately it wasn't addressed so far nor did I get any response
whether I'm right or not. So I would appreciate if you had a look at
this bug report and whether it fixes your problem when you apply the
code fixes which I proposed in the comments.
http://public.kitware.com/Bug/view_all_bug_page.php?filter=20444
regards
Andreas
Kon Z schrieb:
> Hello ALL,
>
> When I use ResampleImageFilter to resample an 3D image with a new
> direction matrix
>
> resampler->SetOutputDirection(directionMatrix);
>
> the filter output shows the specified orientation (with the values I
> specify in the direction matrix):
>
> Direction:
> 0.529919 0.46188 -0.711233
> 0 0.838671 0.544639
> 0.848048 -0.288615 0.444428
>
> However, when I pass resample filter output to a writer connected to
> GDCMImageIO, the saved volume has this orientation (the direction matrix
> is transposed!):
>
> Direction:
> 0.529919 0 0.848048
> 0.46188 0.838671 -0.288615
> -0.711233 0.544639 0.444428
>
> Am I doing something wrong? Or am I not doing something I'm supposed to
> do with the image before passing it to the writer? Can someone please
> explain it to me?
>
> For the moment I use this workaround I found in the ITK Guide:
> itk::EncapsulateMetaData<std::string>(
> resampler->GetOutput()->GetMetaDataDictionary(),
> "0020|0037", // Patient orientation tag.
> directionStream.str().c_str());
>
> where directionStream contains the correct string representation of the
> directionMatrix.
>
> Thanks.
>
> Best regards,
> Kon Z
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
------------------------------
Message: 4
Date: Mon, 18 May 2009 14:34:19 +0200
From: Matilde Gonzalez Preciado <matilde.gonzalez.preciado at gmail.com>
Subject: [Insight-users] Writing mesh to Metafile
To: insight-users at itk.org
Message-ID:
<637f0aa40905180534k5c4e15b2j22b43f1c574e22b4 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I am working with a IndexedTriangleMesh and I want to write it in a vtk file
in order to visualize it easily. I am using itkMeshTovtkPolydata but
SetInput requires a itk::Mesh, I would like to know if it is possible to
convert a IndexedTriangleMesh into a itk::mesh in order to be able to use
this class.
My code is:
typedef itk::Vector<double, 2> PixelType;
typedef unsigned short IndexType;
typedef itk::IndexedTriangleMesh<PixelType, IndexType> OutputMeshType;
itkMeshTovtkPolyData *itkTovtkPolyData = new itkMeshTovtkPolyData();
vtkPolyData* polyData = vtkPolyData::New();
OutputMeshType::Pointer resultMesh ;
resultMesh = ssmCalculator->GetResampledOutputMesh( i ) ;
//Here resultMesh must be itk::Mesh and not itk::IndexedTriangleMesh
itkTovtkPolyData ->SetInput(resultMesh);
polyData = itkTovtkPolyData->GetOutput();
Thank you in advance
--
Matilde GONZALEZ
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Message: 5
Date: Mon, 18 May 2009 14:28:35 +0100
From: "Clark Teresa (North Cumbria Acute Hospitals NHS Trust)"
<teresa.clark at nhs.net>
Subject: [Insight-users] unsubscribe
To: "insight-users at itk.org" <insight-users at itk.org>
Message-ID:
<C88F6C3DC25BB248A039FB16985A42FD3CCF2F92DD at NHS-PCLI-MBC004.AD1.NHS.NET>
Content-Type: text/plain; charset="us-ascii"
unsubsribe
Teresa Clark
Senior Physicist
Medical Physics Department (Radiotherapy section)
Cumberland Infirmary
Newtown Road
Carlisle
CA2 7HY
Tel: 07701018450
Email: teresa.clark at nhs.net
or: teresa.clark at ncumbria-acute.nhs.uk
-----Original Message-----
From: insight-users-bounces at itk.org [mailto:insight-users-bounces at itk.org] On Behalf Of insight-users-request at itk.org
Sent: 13 May 2009 12:30
To: insight-users at itk.org
Subject: Insight-users Digest, Vol 61, Issue 47
Send Insight-users mailing list submissions to
insight-users at itk.org
To subscribe or unsubscribe via the World Wide Web, visit
http://www.itk.org/mailman/listinfo/insight-users
or, via email, send a message with subject or body 'help' to
insight-users-request at itk.org
You can reach the person managing the list at
insight-users-owner at itk.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Insight-users digest..."
Today's Topics:
1. Deformable registration (Youbing Yin)
2. problem while loading corrupted files (Jakub Bican)
3. Re: itk.PyBuffer memory leak (Rick Giuly)
4. itkVTKImageIO does not read back VECTORS image (Denis Shamonin)
5. Problem with image Pixels (Shady Shidfar)
----------------------------------------------------------------------
Message: 1
Date: Tue, 12 May 2009 21:45:26 -0500
From: Youbing Yin <youbing-yin at uiowa.edu>
Subject: [Insight-users] Deformable registration
To: insight-users at itk.org
Message-ID:
<f8f0fd000905121945l189843ch2e9754fbc92af1d1 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi everyone,
I am using Affine and B-spline transformations for matching lung CT images.
However, I found that the registration only with B-spline transform gives a
better result than the one with Affine transform first followed by B-spline
transform. Does anyone have this experience before?
Thanks.
--
Best regards,
Youbing
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Message: 2
Date: Wed, 13 May 2009 08:54:59 +0200
From: Jakub Bican <jakub.bican at matfyz.cz>
Subject: [Insight-users] problem while loading corrupted files
To: Insight <Insight-users at itk.org>
Message-ID:
<1634f88d0905122354p44de3f95r482ec29d25ebf7f at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hello,
we built an image retrieval system and we encountered a problem. In
the bunch of files we have to precess is a large number of corrupter
jpeg files or files with zero length.
We suspect the JPEG image reader class of ITK that it does not close
file handle if it encounters some problem during file reading, because
we run out of file handles on certain linux system after some time of
system our execution.
Do someone have an experience with such behavior?
Thanks, Jakub
------------------------------
Message: 3
Date: Wed, 13 May 2009 01:35:30 -0700
From: Rick Giuly <rgiuly at gmail.com>
Subject: Re: [Insight-users] itk.PyBuffer memory leak
To: Ga?tan Lehmann <gaetan.lehmann at jouy.inra.fr>
Cc: insight users <insight-users at itk.org>
Message-ID: <4A0A8652.90803 at gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
I've now tested invoking garbage collection with gc.collect() at every
iteration and that didn't change the problem. So, my best guess would be
that the image is not deleted when the python object is destroyed. Maybe
a bug?
Ga?tan Lehmann wrote:
>
> Hi Rick,
>
> GetImageFromArray() returns a smart pointer to an image, so the image
> should be deallocated once the python object is destroyed.
> Perhaps the problem is there: the garbage collection my not run fast
> enough.
>
> The right way to go may be to implement PyBuffer as a filter which reuse
> the output image, as all the filters in itk.
>
> For the Delete() method: you shouldn't use it in python (and I can't see
> any case for use it but the internal memory management in c++). In the
> latest version of wrapitk (the one hosted at googlecode), Delete() and
> the other methods related to smart pointers are hidden.
>
> Regards,
>
> Ga?tan
>
>
>
> Le 11 mai 09 ? 05:43, Rick Giuly a ?crit :
>
>>
>> Hello All,
>>
>> It seems that converter.GetImageFromArray(inputNumpyVolume) allocates
>> memory in some way and never releases it. When I tried using Delete()
>> the program actually crashed silently after one iteration.
>>
>> Test code is below. (I'm running this on ubuntu, and the itk package
>> is from Paul Novo's site.)
>>
>> Is there some way to release memory?
>>
>>
>>
>> import itk
>> import numpy
>>
>> for i in range(10000):
>>
>> print i
>>
>> ImageType = itk.Image[itk.F, 3]
>> converter = itk.PyBuffer[ImageType]
>>
>> inputNumpyVolume = numpy.ones((100, 100, 200))
>> inputVolume = converter.GetImageFromArray(inputNumpyVolume)
>> #inputVolume.Delete()
>>
>>
>>
>> ----------
>> Thanks,
>> --Rick
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-users
>
------------------------------
Message: 4
Date: Wed, 13 May 2009 12:28:29 +0200 (CEST)
From: "Denis Shamonin" <dshamoni at science.uva.nl>
Subject: [Insight-users] itkVTKImageIO does not read back VECTORS
image
To: insight-users at itk.org
Message-ID:
<31171.145.88.209.33.1242210509.squirrel at webmail.science.uva.nl>
Content-Type: text/plain;charset=iso-8859-1
Hi,
I think I found a bug in itkVTKImageIO. It is not possible to read back
vector images which were created by itkVTKImageIO.
You end up in an infinite loop during
InternalReadImageInformation(std::ifstream& file)
in the for loop starting at Line 234 itkVTKImageIO.cxx
With images of type:
itk::Image< itk::Vector<float, 3>, 3 >
Bug description:
http://www.itk.org/Bug/view.php?id=9013
Would it be possible to fix it for the coming release?
-Denis
------------------------------
Message: 5
Date: Wed, 13 May 2009 04:23:28 -0700 (PDT)
From: Shady Shidfar <shady_shidfar at yahoo.com>
Subject: [Insight-users] Problem with image Pixels
To: insight users <insight-users at itk.org>
Message-ID: <631165.68649.qm at web110302.mail.gq1.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi everyone,?I'm having a problem with converting ITK image into VTK and because I'm not sure if the problem is related to ITK or VTK I'm sending this mail to both forums hoping someone can help.
I'm converting my ITK image to a VTK object using itkImageToVTKImageFilter. The ?image has the origin of 0,0 and spacing 1,1. The problem is that?it seems that?the edge pixels of the image I view in VTK have spacing of 0.5,1 or 1,0.5 , So they look like a half pixel. This to me looks like a bug. I'm not sure if the problem is with pixel dimentions in VTK or ITK or it has to do with the itkImageToVTKImageFilter. I'm attaching the image file and a picture of what I view in VTK and the same image?viewed in ImageJ. It seems like the image has been slightly cropped. It can be seen that data is obviously being lost at the edges. Can someone please help me with this? Any idea what the problem is and how can I fix it.
?
Thanks in advance
Shaadi?
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