[Insight-users] Insight-users Digest, Vol 76, Issue 8
Peng, Hanchuan, Ph.D.
pengh at janelia.hhmi.org
Wed Aug 4 07:51:27 EDT 2010
thanks!
On 8/4/10 6:27 AM, "insight-users-request at itk.org"
<insight-users-request at itk.org> wrote:
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> Today's Topics:
>
> 1. Re: artifact removal in CT (Bill Lorensen)
> 2. git clone missing files? (David Doria)
> 3. sf (paniwani)
> 4. Creating 3D RGB image from Enum Image (paniwani)
> 5. Mean shift clustering for 3D image example (liuji710)
> 6. Re: git clone missing files? (Bill Lorensen)
> 7. MICCAI: Microscopy Image Analysis Tutorial (Luis Ibanez)
> 8. DicomImageReadWrite error itkgdcm.lib(gdcmUtil.obj) : error
> LNK2019 (Chanukya Krishna Chama)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 3 Aug 2010 16:46:38 -0400
> From: Bill Lorensen <bill.lorensen at gmail.com>
> Subject: Re: [Insight-users] artifact removal in CT
> To: somi <seesomi at gmail.com>
> Cc: insight-users at itk.org
> Message-ID:
> <AANLkTimLrZYJh4bXgyXakXVPVWLR0RCJ+w1SfNCPCGVq at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Sorry, no,
>
> Bill
>
>
> On Tue, Aug 3, 2010 at 2:20 PM, somi <seesomi at gmail.com> wrote:
>> Hi Bill,
>> I searched for the metal atrtifact removal in CT. As you mentioned most of
>> the algorithms work on the sinogram .
>> However I only have access to CT data not the raw data.
>> Is there any implementation of inverse radon transform in ITK to get
>> sinogram from CT ?
>> Thanks,
>> Somi
>>
>> On Tue, Aug 3, 2010 at 12:36 PM, Bill Lorensen <bill.lorensen at gmail.com>
>> wrote:
>>>
>>> These types of artifacts are usually removed during the
>>> reconstruction. Do a goole search on metal atrifacts ct.
>>>
>>>
>>> On Tue, Aug 3, 2010 at 10:24 AM, somi <seesomi at gmail.com> wrote:
>>>> Hi,
>>>> I have a CT image with lots of scatter in it due to presence of some
>>>> metal
>>>> parts while scanning. See attached image.
>>>> Does ITK have any filters for this kind of artifact removal ? Any
>>>> suggestions for removal ?
>>>> Thanks,
>>>> Somi
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.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: 2
> Date: Tue, 3 Aug 2010 18:49:01 -0400
> From: David Doria <daviddoria+itk at gmail.com>
> Subject: [Insight-users] git clone missing files?
> To: ITK <insight-users at itk.org>
> Message-ID:
> <AANLkTinTJe0T0M2m+jqUGVYZfPBNe1d65dgg9xiopo+V at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I ran:
>
> git clone git://itk.org/ITK.git
>
> and then built ITK with no apparently issues. However, I then went to
> ran some of my code and got lots of "missing file" errors.
>
> Examples of missing files include:
> itkScalarImageToListAdaptor.h
> itkSampleMeanShiftClusteringFilter.h
>
> Searching for these files in my ITK src directory returns nothing:
>
> [doriad at localhost ITK]$ pwd
> /home/doriad/src/ITK
> [doriad at localhost ITK]$ find . -name itkSampleMean*
> [doriad at localhost ITK]$
>
> These files seem to still exist (according to
> http://www.itk.org/Doxygen/html/classitk_1_1Statistics_1_1SampleMeanShiftClust
> eringFilter.html).
>
> Any idea why these files didn't get downloaded during the clone?
>
> Thanks,
>
> David
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 3 Aug 2010 18:03:13 -0700 (PDT)
> From: paniwani <paniwani at gmail.com>
> Subject: [Insight-users] sf
> To: insight-users at itk.org
> Message-ID: <1280883793490-5370753.post at n2.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
>
> Hi. I have a 3D image that serves as a "map" for another 3D image. It
> indicates the type of voxel at every location in the image. The type
> definitions for the voxel type image and regular image are as follows:
>
> enum VoxelType {
> Stool=1,
> Air=2,
> Tissue=3,
> Unclassified=4,
> StoolAir=5,
> TissueAir=6,
> TissueStool=7,
> ThinStool=8
> };
>
> typedef itk::Image VoxelTypeImage;
> typedef Float4 PixelType;
> typdef itk::Image ImageType;
>
> Currently, I can output both the regular image and the voxel type image as
> Analyze files and view them using ImageJ. However, I would like to create a
> colored 3D version of the voxel type image and view it using ImageJ as well.
>
> What file type would be suitable to view such a 3D RGB image? How would I
> write such a file?
>
> I have seen this in another post:
>
> "3) Note that you can do this a lot easier
> with the new filter:
>
> itkScalarToRGBColormapImageFilter.txx
>
> and the color map:
>
> itkRedColormapFunctor.h
>
> You will find this class described in
> the Insight Journal paper:
>
> http://www.insight-journal.org/browse/publication/285"
>
> However, whenever I include this filter in my header file C++ says it cannot
> find the file. I was able to find the file online and copy it into my source
> directory, but even then the itkRedColormapFunctor.h could not be found. Is
> there something unique to including and using this filter? Even if I could
> get C++ to recognize the filter, how exactly do I go about using it to
> create this 3D RGB map?
>
> Thanks in advance.
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/sf-tp5370753p5370753.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 3 Aug 2010 18:08:50 -0700 (PDT)
> From: paniwani <paniwani at gmail.com>
> Subject: [Insight-users] Creating 3D RGB image from Enum Image
> To: insight-users at itk.org
> Message-ID: <1280884130656-5370770.post at n2.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
>
> Hi. I have a 3D image that serves as a "map" for another 3D image. It
> indicates the type of voxel at every location in the image. The type
> definitions for the voxel type image and regular image are as follows:
>
> enum VoxelType {
> Stool=1,
> Air=2,
> Tissue=3,
> Unclassified=4,
> StoolAir=5,
> TissueAir=6,
> TissueStool=7,
> ThinStool=8
> };
>
> typedef itk::Image<VoxelType, 3> VoxelTypeImage;
> typedef Float4 PixelType;
> typdef itk::Image<PixelType, 3> ImageType;
>
> Currently, I can output both the regular image and the voxel type image as
> Analyze files and view them using ImageJ. However, I would like to create a
> colored 3D version of the voxel type image and view it using ImageJ as well.
> What file type would be suitable to view such a 3D RGB image? How would I
> write such a file? I have seen this in another post:
>
> "Note that you can do this a lot easier with the new filter:
> itkScalarToRGBColormapImageFilter.txx
>
> and the color map: itkRedColormapFunctor.h
>
> You will find this class described in the Insight Journal paper:
> http://www.insight-journal.org/browse/publication/285"
>
> However, whenever I include this filter in my header file C++ says it cannot
> find the file. I was able to find the file online and copy it into my source
> directory, but even then the itkRedColormapFunctor.h could not be found. Is
> there something unique to including and using this filter?
>
> Even if I could get C++ to recognize the filter, how exactly do I go about
> using it to create this 3D RGB map? Thanks in advance.
> --
> View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/Creating-3D-RGB-image-from-Enum
> -Image-tp5370770p5370770.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 4 Aug 2010 09:43:45 +0800 (CST)
> From: liuji710 <liuji710 at 163.com>
> Subject: [Insight-users] Mean shift clustering for 3D image example
> To: insight-users at itk.org
> Message-ID: <9a066c.a0c3.12a3ac4bc20.Coremail.liuji710 at 163.com>
> Content-Type: text/plain; charset="gbk"
>
> I am trying to make an example out of the Test for
> SampleMeanShiftClusteringFilter.
> http://www.itk.org/Wiki/ITK/InsightClopedia/MeanShiftClustering
> the "SampleMeanShiftClustering.cxx" could work well on the 2D image.But to 3D
> medical image ,it turns very slow and nearly can't work.The image size is
> 256*256*118.
>
> this is the first time to use the "SampleMeanShiftClustering.cxx". .And I
> don't Modify the "SampleMeanShiftClustering.cxx",so all the data is the same
> as the source codes.
>
> I want the use the "SampleMeanShiftClustering.cxx" to work with the 3D
> medical image ,so ask for help.
>
> Thanks,
>
> Liu
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> ------------------------------
>
> Message: 6
> Date: Tue, 3 Aug 2010 23:38:59 -0400
> From: Bill Lorensen <bill.lorensen at gmail.com>
> Subject: Re: [Insight-users] git clone missing files?
> To: David Doria <daviddoria+itk at gmail.com>
> Cc: ITK <insight-users at itk.org>
> Message-ID:
> <AANLkTikkq=Z3DVtbSFPBzsYaSvCVLTrq_UFHw1+wQOXW at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> David,
>
> itkv4 is using the new statistics framework that was in Review/Statistics.
>
> It IS NOT backward compatible with the previous Statistics classes.
>
> There is a migration guide here:
> http://www.itk.org/Wiki/Proposals:Refactoring_Statistics_Framework_2007_Migrat
> ion_Users_Guide
>
> Also, you can probably expect some instability in the itkv4 git
> repository since this is a new effort
>
> Bill
>
> On Tue, Aug 3, 2010 at 6:49 PM, David Doria <daviddoria+itk at gmail.com> wrote:
>> I ran:
>>
>> git clone git://itk.org/ITK.git
>>
>> and then built ITK with no apparently issues. However, I then went to
>> ran some of my code and got lots of "missing file" errors.
>>
>> Examples of missing files include:
>> itkScalarImageToListAdaptor.h
>> itkSampleMeanShiftClusteringFilter.h
>>
>> Searching for these files in my ITK src directory returns nothing:
>>
>> [doriad at localhost ITK]$ pwd
>> /home/doriad/src/ITK
>> [doriad at localhost ITK]$ find . -name itkSampleMean*
>> [doriad at localhost ITK]$
>>
>> These files seem to still exist (according to
>> http://www.itk.org/Doxygen/html/classitk_1_1Statistics_1_1SampleMeanShiftClus
>> teringFilter.html).
>>
>> Any idea why these files didn't get downloaded during the clone?
>>
>> Thanks,
>>
>> David
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.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: 7
> Date: Wed, 4 Aug 2010 06:19:20 -0400
> From: Luis Ibanez <luis.ibanez at kitware.com>
> Subject: [Insight-users] MICCAI: Microscopy Image Analysis Tutorial
> To: itk <Insight-users at itk.org>, Insight Developers
> <Insight-developers at itk.org>
> Message-ID:
> <AANLkTikhHSzpDRn4o+RKZ8xwHWqHRwvZ_wW434RJBMAF at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> At MICCAI 2010, you are invited to attend the
> tutorial on:
>
> Microscopy Image Analysis
> http://penglab.janelia.org/proj/miccai2010/
>
> Sept 24, 2010
>
> An outline of the Tutorial content is available at:
> http://penglab.janelia.org/proj/miccai2010/Outline.html
>
>
> This tutorial will introduce the recent development and techniques of
> 2D, 3D, 4D, and 5D microscopic image analysis and visualization, with
> a central theme of the newly emerging field of bioimage informatics.
>
> We will discuss new and exciting challenges in 2D/3D/4D/5D biological
> and microscopic image computing, as well as large-scale (gigabyte-size
> image) visualization and interaction, - with a focus on microscopy images
> but can be generally useful for other large biomedical images.
>
> We are also going to give a relatively detailed tutorial (and demonstration)
>
> on how to use some of the most advanced & powerful 3D/4D/5D image
> visualization assisted tools for quantitative analysis.
>
>
> Instructors:
>
> * Hanchuan Peng - Janelia HHMI
> * Jens Rittscher - GE Research
> * Tianming Liu - University of Georgia
> * Fuhui Long - Janelia HHMI
> * Sean Megason - Harvard Medical School
> * Luis Ibanez - Kitware
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> ------------------------------
>
> Message: 8
> Date: Wed, 4 Aug 2010 15:44:08 +0530 (IST)
> From: Chanukya Krishna Chama <chanukya_chess at yahoo.co.in>
> Subject: [Insight-users] DicomImageReadWrite error
> itkgdcm.lib(gdcmUtil.obj) : error LNK2019
> To: insight-users at itk.org
> Message-ID: <384789.52352.qm at web95402.mail.in2.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> I'm using ITK 3.20 & Visual Studio 2010 along with cmake to run sample
> DicomImageReadWrite example program in ITK folder.
>
> After including all the *.lib files in ITK\lib\ in Input of Linker in visual
> studio, i'm getting the below error while debugging
>
> itkgdcm.lib(gdcmUtil.obj) : error LNK2019: unresolved external symbol
> _SnmpUtilVarBindFree at 4 referenced in function "int __cdecl
> gdcm::GetMacAddrSys(unsigned char *)" (?GetMacAddrSys at gdcm@@YAHPAE at Z)
>
> How to remove this error ?
>
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> ------------------------------
>
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>
> End of Insight-users Digest, Vol 76, Issue 8
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