Insight Toolkit Users - Image registration and segmentation toolkit ()

x0_y0_0 | 1 Jun 2009 05:19

some problem about 3D RAW convert to DICOM series?

hi,everyone,

I have a dataset of 3D RAW ,and its Parameters: 256*256*256; 16bits, effective bits are 12 bits. I want to convert it to 256 pieces DICOM image. I goole in the Internet,and someone use DicomSeriesReadImageWrite2.cxx to deal with it ,and I tried but failed.

Input: DicomSeriesReadImageWrite2.exe G:\DicomSeriesReadImageWrite2\debug\alta G:\DicomSeriesReadImageWrite2\debug\output

Inputfile-atlas_data.mhd:

               NDims = 3
               ElementByteOrderMSB = False
               ElementSpacing = 1 1 1
               DimSize = 256 256 256
               ElementType = MET_UCHAR
               Offset = 13.4 275 43.2
               ElementDataFile = atlas_data.raw

error:

itkGDCMSeriesFileNames.cxx:GDCMSeriesFileNames[01834BB8]:No Series were found.

Could anybody help me ? thanks!

regards,

mexiao

业务订单流失怎么办？

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Sgouritsa, Eleni | 1 Jun 2009 05:52

itkScalarChanAndVeseSparseLevelSetImageFilter

Hello,
I know that the review folder of the new release (3.14) is not stable yet but I would just like to give two comments:

1. I found an inconsistency between the template arguments of the itkScalarChanAndVeseSparseLevelSetImageFilter.h and the itkScalarChanAndVeseSparseLevelSetImageFilter.txx.
Specifically, in the header file, the template is :
template < class TInputImage, class TFeatureImage, class TOutputImage, class TFunction,
class TSharedData, typename TIdCell = unsigned int >
whereas in the txx it is:
template < class TInput, class TFeature, class TFunction,
class TOutputPixel, class TSharedData, typename TIdCell >
There is a change in the order of the 3rd and 4th argument.

2. I can not find this class (itkScalarChanAndVeseSparseLevelSetImageFilter) incuded in the CMakeLists of the review folder

Regards,
Lena

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alex gouaillard | 1 Jun 2009 06:34

Re: itkScalarChanAndVeseSparseLevelSetImageFilter

hi eleni,

we'll take a look tomorrow.

thanks for the feedback.

alex.

On May 31, 2009, at 11:52 PM, Sgouritsa, Eleni wrote:

Hello,
I know that the review folder of the new release (3.14) is not stable yet but I would just like to give two comments:

1. I found an inconsistency between the template arguments of the itkScalarChanAndVeseSparseLevelSetImageFilter.h and the itkScalarChanAndVeseSparseLevelSetImageFilter.txx.
Specifically, in the header file, the template is :
template < class TInputImage, class TFeatureImage, class TOutputImage, class TFunction,
class TSharedData, typename TIdCell = unsigned int >
whereas in the txx it is:
template < class TInput, class TFeature, class TFunction,
class TOutputPixel, class TSharedData, typename TIdCell >
There is a change in the order of the 3rd and 4th argument.

2. I can not find this class (itkScalarChanAndVeseSparseLevelSetImageFilter) incuded in the CMakeLists of the review folder

Regards,
Lena

<ATT00001.txt>

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Sam Sun | 1 Jun 2009 06:34

InvertIntensityImageFilter

Can you please help me to see if I apply InvertIntensityImageFilter correctly or not as in enclosed code snippet?

I have no idea why the output image is blank. Your kind help is greatly appreciated.

// Invert intensity of the image
    itk::InvertIntensityImageFilter<InputImageType,InputImageType>::Pointer invertImage;
    invertImage = itk::InvertIntensityImageFilter<InputImageType,InputImageType>::New();
    invertImage->SetInput(inputImage->GetOutput());

    try
        {
            invertImage->Update();
        }
        catch( itk::ExceptionObject & exception )
        {
            std::cout << "Problems in shrinking the image" << std::endl;
            std::cout << exception << std::endl;
            return 1;
        }
// End of invert intensity

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Sgouritsa, Eleni | 1 Jun 2009 11:00

Re: itkScalarChanAndVeseSparseLevelSetImageFilter

Hello,
finally the second issue was my fault (I just had a problem while including the header files of the review folder).
For the first, the inconsistency is just a matter of name. The code runs correctly, just the name assignement in the txx is a little misleading.

Thank you very much,
Lena

-----Original Message-----
From: alex gouaillard [mailto:alexandre_gouaillard-nES/7uYZTuC+fmr0zi+kZQ@public.gmane.org]
Sent: Sun 5/31/2009 11:34 PM
To: Sgouritsa, Eleni
Cc: insight-users-RyaoCGfWeh4@public.gmane.org
Subject: Re: [Insight-users] itkScalarChanAndVeseSparseLevelSetImageFilter

hi eleni,

we'll take a look tomorrow.

thanks for the feedback.

alex.

On May 31, 2009, at 11:52 PM, Sgouritsa, Eleni wrote:

> Hello,
> I know that the review folder of the new release (3.14) is not
> stable yet but I would just like to give two comments:
>
> 1. I found an inconsistency between the template arguments of the
> itkScalarChanAndVeseSparseLevelSetImageFilter.h and the
> itkScalarChanAndVeseSparseLevelSetImageFilter.txx.
> Specifically, in the header file, the template is :
> template < class TInputImage, class TFeatureImage, class
> TOutputImage, class TFunction,
> class TSharedData, typename TIdCell = unsigned int >
> whereas in the txx it is:
> template < class TInput, class TFeature, class TFunction,
> class TOutputPixel, class TSharedData, typename TIdCell >
> There is a change in the order of the 3rd and 4th argument.
>
> 2. I can not find this class
> (itkScalarChanAndVeseSparseLevelSetImageFilter) incuded in the
> CMakeLists of the review folder
>
> Regards,
> Lena
>
> <ATT00001.txt>

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Raquel Itk | 1 Jun 2009 18:57

DICOM: problem with the pixel values

Hi,
I’m working at Project in my University. I use Dicom Image of CT lungs.
I can get the value of the pixels with an iterator. There are negative in a lot of cases.
I use too Matlab. When I display my image with this software I match that the pixels values are different than with the iterator.
I define the type of the pixels in Dicom in this way:
typedef signed short InputPixelType;

I would prefer that píxel values with the Itk would have the same value that the have with Matlab but I don’t know how I can define the pixels.
I tried rescale the image but I din’t get the result that I would like.

Can anybody help me??

Sorry if my English is no perfect.

Thanks. Raquel

Matlab : [-2000, 2286]
ITK:[-3024,14360]

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Daniel Blezek | 1 Jun 2009 20:17

Re: DICOM: problem with the pixel values

Hi Raquel,

When you load images using Matlab, it does not honor the RescaleSlope and RescaleIntercept tags. Your data in Matlab will always be positive. ITK honors these flags and the images will have negative values (indicating a density less than water). You can achieve the same intensities if you use this Matlab code

function [Image Header] = ReadDICOM ( fn )
% Load a DICOM file and apply slope and intecept

Header = dicominfo ( fn );
Image = Header.RescaleSlope * double ( dicomread ( Header ) ) + Header.RescaleIntercept;
return

Your DICOM and ITK should have the same intensities. However, be aware that ITK and DICOM may horizontally flip the images in different ways.

Cheers,
-dan

On 6/1/09 11:57 AM, "Raquel Itk" <raquelitk-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

Hi,
I’m working at Project in my University. I use Dicom Image of CT lungs.
I can get the value of the pixels with an iterator. There are negative in a lot of cases.
I use too Matlab. When I display my image with this software I match that the pixels values are different than with the iterator.
I define the type of the pixels in Dicom in this way:
typedef signed short InputPixelType;

I would prefer that píxel values with the Itk would have the same value that the have with Matlab but I don’t know how I can define the pixels.
I tried rescale the image but I din’t get the result that I would like.

Can anybody help me??

Sorry if my English is no perfect.

Thanks. Raquel

Matlab : [-2000, 2286]
ITK:[-3024,14360]

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--
Daniel Blezek, PhD
Medical Imaging Informatics Innovation Center

P 127 or (77) 8 8886
T 507 538 8886
E blezek.daniel-3dqG1TfY5Cg@public.gmane.org

Mayo Clinic
200 First St. S.W.
Harwick SL-44
Rochester, MN 55905
mayoclinic.org

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Gaëtan Lehmann | 1 Jun 2009 23:21

Re: [Insight-developers] Tagging and Branching : CVS is Open


Luis, Wes,

It works now - I've just committed my fixes.

Thank you,

Gaëtan

Le 30 mai 09 à 17:20, Luis Ibanez a écrit :

>
> Gaetan,
>
>
>
>    The CVS repository is now open.
>
>
> Please let us know if you find any problem.
>
>
>   Thanks
>
>
>      Luis
>
>
>
> -------------------
> Wes Turner wrote:
>> Hi Gaetan,
>> I apologize for the delay.  As my note suggested, I had assumed it  
>> would be unlocked by now ... unfortunately, Luis needs to do it and  
>> he is at NIH today (and yesterday which probably explains the  
>> delay).  I expect that he only has sporadic access to the  
>> Internet.  He will be back this evening, so this should not be  
>> ongoing.  - Wes
>> 2009/5/29 Gaëtan Lehmann <gaetan.lehmann@...
<mailto:gaetan.lehmann@... 
>> >>
>>    Le 27 mai 09 à 23:46, Wes Turner a écrit :
>>        All,
>>        I finished the tagging and branching and am working on  
>> packaging
>>        up the delivery.  You can expect Luis to reopen the repository
>>        for new checkins sometime tomorrow.
>>    Hi Wes,
>>    Cvs repository seems to be still locked.
>>    Aren't we allowed to commit again since the tagging and branching?
>>    Regards,
>>    Gaëtan
>>    --     Gaëtan Lehmann
>>    Biologie du Développement et de la Reproduction
>>    INRA de Jouy-en-Josas (France)
>>    tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
>>    http://voxel.jouy.inra.fr  http://www.mandriva.org
>>    http://www.itk.org  http://www.clavier-dvorak.org
>> -- 
>> Wesley D. Turner, Ph.D.
>> Kitware, Inc.
>> R&D Engineer
>> 28 Corporate Drive
>> Clifton Park, NY 12065-8662
>> Phone: 518-371-3971 x120
>> ------------------------------------------------------------------------
>> _______________________________________________
>> 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-developers

-- 
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
http://voxel.jouy.inra.fr  http://www.mandriva.org
http://www.itk.org  http://www.clavier-dvorak.org

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Sgouritsa, Eleni | 2 Jun 2009 01:33

Re: itkScalarChanAndVeseSparseLevelSetImageFilter

Hi,

I have two more questions.
1. In the insight journal code there was an option SetReverseExpansionDirection to control if the expansion of the level set will be inwards or outwards. How can I do it using the itkScalarChanAndVeseSparseLevelSetImageFilter of 3.14 release?

2. I still have a problem when my 3D data have negative origin.

Thanks and regards,
Lena

-----Original Message-----
From: Sgouritsa, Eleni
Sent: Mon 6/1/2009 4:00 AM
To: alex gouaillard
Cc: insight-users-RyaoCGfWeh4@public.gmane.org
Subject: RE: [Insight-users] itkScalarChanAndVeseSparseLevelSetImageFilter

Hello,
finally the second issue was my fault (I just had a problem while including the header files of the review folder).
For the first, the inconsistency is just a matter of name. The code runs correctly, just the name assignement in the txx is a little misleading.

Thank you very much,
Lena

-----Original Message-----
From: alex gouaillard [mailto:alexandre_gouaillard-nES/7uYZTuC+fmr0zi+kZQ@public.gmane.org]
Sent: Sun 5/31/2009 11:34 PM
To: Sgouritsa, Eleni
Cc: insight-users-RyaoCGfWeh4@public.gmane.org
Subject: Re: [Insight-users] itkScalarChanAndVeseSparseLevelSetImageFilter

hi eleni,

we'll take a look tomorrow.

thanks for the feedback.

alex.

On May 31, 2009, at 11:52 PM, Sgouritsa, Eleni wrote:

> Hello,
> I know that the review folder of the new release (3.14) is not
> stable yet but I would just like to give two comments:
>
> 1. I found an inconsistency between the template arguments of the
> itkScalarChanAndVeseSparseLevelSetImageFilter.h and the
> itkScalarChanAndVeseSparseLevelSetImageFilter.txx.
> Specifically, in the header file, the template is :
> template < class TInputImage, class TFeatureImage, class
> TOutputImage, class TFunction,
> class TSharedData, typename TIdCell = unsigned int >
> whereas in the txx it is:
> template < class TInput, class TFeature, class TFunction,
> class TOutputPixel, class TSharedData, typename TIdCell >
> There is a change in the order of the 3rd and 4th argument.
>
> 2. I can not find this class
> (itkScalarChanAndVeseSparseLevelSetImageFilter) incuded in the
> CMakeLists of the review folder
>
> Regards,
> Lena
>
> <ATT00001.txt>

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Luis Ibanez | 2 Jun 2009 03:39

Re: itkScalarChanAndVeseSparseLevelSetImageFilter


Hi Lena,

Could you please be more specific about your problem report on
item (2) ?

Is there a chance that you can report this in a form that
we could reproduce ?

    Thanks

       Luis

-----------------------------
Sgouritsa, Eleni wrote:
> Hi,
> 
> I have two more questions.
> 1. In the insight journal code there was an option 
> SetReverseExpansionDirection to control if the expansion of the level 
> set will be inwards or outwards. How can I do it using the  
> itkScalarChanAndVeseSparseLevelSetImageFilter of 3.14 release?
> 
> 2. I still have a problem when my 3D data have negative origin.
> 
> Thanks and regards,
> Lena
> 
> -----Original Message-----
> From: Sgouritsa, Eleni
> Sent: Mon 6/1/2009 4:00 AM
> To: alex gouaillard
> Cc: insight-users@...
> Subject: RE: [Insight-users] itkScalarChanAndVeseSparseLevelSetImageFilter
> 
> Hello,
> finally the second issue was my fault (I just had a problem while 
> including the header files of the review folder).
> For the first, the inconsistency is just a matter of name. The code runs 
> correctly, just the name assignement in the txx is a little misleading.
> 
> Thank you very much,
> Lena
> 
> 
> -----Original Message-----
> From: alex gouaillard [mailto:alexandre_gouaillard@...]
> Sent: Sun 5/31/2009 11:34 PM
> To: Sgouritsa, Eleni
> Cc: insight-users@...
> Subject: Re: [Insight-users] itkScalarChanAndVeseSparseLevelSetImageFilter
> 
> hi eleni,
> 
> we'll take a look tomorrow.
> 
> thanks for the feedback.
> 
> alex.
> 
> On May 31, 2009, at 11:52 PM, Sgouritsa, Eleni wrote:
> 
>  > Hello,
>  > I know that the review folder of the new release (3.14) is not 
>  > stable yet but I would just like to give two comments:
>  >
>  > 1. I found an inconsistency between the template arguments of the 
>  > itkScalarChanAndVeseSparseLevelSetImageFilter.h and the 
>  > itkScalarChanAndVeseSparseLevelSetImageFilter.txx.
>  > Specifically, in the header file, the template is :
>  > template < class TInputImage, class TFeatureImage, class 
>  > TOutputImage, class TFunction,
>  >   class TSharedData, typename TIdCell = unsigned int >
>  > whereas in the txx it is:
>  > template < class TInput, class TFeature, class TFunction,
>  > class TOutputPixel, class TSharedData, typename TIdCell >
>  > There is a change in the order of the 3rd and 4th argument.
>  >
>  > 2. I can not find this class 
>  > (itkScalarChanAndVeseSparseLevelSetImageFilter)  incuded in the 
>  > CMakeLists of the review folder
>  >
>  > Regards,
>  > Lena
>  >
>  > <ATT00001.txt>
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _____________________________________
> 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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