From kanmaniguna at gmail.com  Thu May  2 07:09:13 2019
From: kanmaniguna at gmail.com (kanmaniguna)
Date: Thu, 2 May 2019 04:09:13 -0700 (MST)
Subject: [ITK] [ITK-users] Create STL file from DICOM 2D series of images
Message-ID: <1556795353337-0.post@n2.nabble.com>

HI

I am new to ITK and VTK but i am able to build the ITK and VTK.

I have set of 2D DICOM series images around 425. I need to create STL file
from dicom 2d images.

What are steps are invloved to create STL file from DICOM 2D images.

Many Thanks.



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From dzenanz at gmail.com  Thu May  2 10:28:19 2019
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 2 May 2019 10:28:19 -0400
Subject: [ITK] [ITK-users] Create STL file from DICOM 2D series of images
In-Reply-To: <1556795353337-0.post@n2.nabble.com>
References: <1556795353337-0.post@n2.nabble.com>
Message-ID: <CAPf2UMQNeFVeei8rVDHwSuix2WFc026WnkVTLq7UeajpLGog5A@mail.gmail.com>

Hi,

what might better suit your needs is an application which combines them.
Slicer has tools to import DICOM, segment the image, and write the result
in .stl format. And here is a tutorial for just such a thing:
https://discourse.slicer.org/t/new-video-tutorial-for-segment-editor-lumbar-spine-segmentation-for-3d-printing/700


Regards,
D?enan

On Thu, May 2, 2019 at 7:09 AM kanmaniguna <kanmaniguna at gmail.com> wrote:

> HI
>
> I am new to ITK and VTK but i am able to build the ITK and VTK.
>
> I have set of 2D DICOM series images around 425. I need to create STL file
> from dicom 2d images.
>
> What are steps are invloved to create STL file from DICOM 2D images.
>
> Many Thanks.
>
>
>
> --
> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
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From kanmaniguna at gmail.com  Thu May  2 12:25:27 2019
From: kanmaniguna at gmail.com (kanmaniguna)
Date: Thu, 2 May 2019 09:25:27 -0700 (MST)
Subject: [ITK] [ITK-users] Create STL file from DICOM 2D series of images
In-Reply-To: <CAPf2UMQNeFVeei8rVDHwSuix2WFc026WnkVTLq7UeajpLGog5A@mail.gmail.com>
References: <1556795353337-0.post@n2.nabble.com>
 <CAPf2UMQNeFVeei8rVDHwSuix2WFc026WnkVTLq7UeajpLGog5A@mail.gmail.com>
Message-ID: <1556814327051-0.post@n2.nabble.com>

HI

This is my college assignment. 
So i need go with ITK or VTK.

Looking forward your reply.



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From sean at rogue-research.com  Thu May  2 15:11:15 2019
From: sean at rogue-research.com (Sean McBride)
Date: Thu, 2 May 2019 15:11:15 -0400
Subject: [ITK] [ITK-users] Create STL file from DICOM 2D series of images
In-Reply-To: <1556814327051-0.post@n2.nabble.com>
References: <1556795353337-0.post@n2.nabble.com>
 <CAPf2UMQNeFVeei8rVDHwSuix2WFc026WnkVTLq7UeajpLGog5A@mail.gmail.com>
 <1556814327051-0.post@n2.nabble.com>
Message-ID: <20190502191115.175328891@mail.rogue-research.com>

On Thu, 2 May 2019 09:25:27 -0700, kanmaniguna said:

>This is my college assignment. 

DICOM files are a structured grid:
<https://en.wikipedia.org/wiki/Regular_grid>

STL files are a triangle mesh:
<https://en.wikipedia.org/wiki/Triangle_mesh>

You'll need to research how to make the latter from the former.

Cheers,

-- 
____________________________________________________________
Sean McBride, B. Eng                 sean at rogue-research.com
Rogue Research                        www.rogue-research.com 
Mac Software Developer              Montr?al, Qu?bec, Canada


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From srbn.ghosh99 at gmail.com  Tue May  7 14:34:20 2019
From: srbn.ghosh99 at gmail.com (Shrabani Ghosh)
Date: Tue, 7 May 2019 11:34:20 -0700 (MST)
Subject: [ITK] [ITK-users] Image conversion from 3D volume  to 2D slices
Message-ID: <1557254060777-0.post@n2.nabble.com>

Hello Everyone,

I am trying to extract 2D slices from a 3d Image volume. I was able to do
that using ImageReadExtractWrite.cxx. But when I see the 2D slices, they are
distorted. They do not look like the 2d original 2D slices from where 3D
volume created. Is there any other way to get the original 3D slices?

Thank You



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From dzenanz at gmail.com  Tue May  7 15:46:03 2019
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 7 May 2019 15:46:03 -0400
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <1557254060777-0.post@n2.nabble.com>
References: <1557254060777-0.post@n2.nabble.com>
Message-ID: <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>

Hi Shrabani,

you should try different direction matrix collapse strategies:
https://itk.org/Doxygen/html/classitk_1_1ExtractImageFilter.html#a5b3bcfa552d8ad7cf509e32209aadc13

Regards,
D?enan

On Tue, May 7, 2019 at 2:43 PM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
wrote:

> Hello Everyone,
>
> I am trying to extract 2D slices from a 3d Image volume. I was able to do
> that using ImageReadExtractWrite.cxx. But when I see the 2D slices, they
> are
> distorted. They do not look like the 2d original 2D slices from where 3D
> volume created. Is there any other way to get the original 3D slices?
>
> Thank You
>
>
>
> --
> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
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From srbn.ghosh99 at gmail.com  Tue May  7 18:35:54 2019
From: srbn.ghosh99 at gmail.com (Shrabani Ghosh)
Date: Tue, 7 May 2019 15:35:54 -0700 (MST)
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
References: <1557254060777-0.post@n2.nabble.com>
 <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
Message-ID: <1557268554107-0.post@n2.nabble.com>

Can you recommend any similar example which has used this function?



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From dzenanz at gmail.com  Tue May  7 21:14:48 2019
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 7 May 2019 21:14:48 -0400
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <1557268554107-0.post@n2.nabble.com>
References: <1557254060777-0.post@n2.nabble.com>
 <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
 <1557268554107-0.post@n2.nabble.com>
Message-ID: <CAPf2UMQjZFitRaWuP=NVFJKLuQTdKF2sBDfQj6w6kcB7eaQPOQ@mail.gmail.com>

How about this one:
https://itk.org/Doxygen/html/SphinxExamples_2src_2Filtering_2ImageGrid_2ProcessA2DSliceOfA3DImage_2Code_8cxx-example.html#_a4


On Tue, May 7, 2019 at 6:35 PM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
wrote:

> Can you recommend any similar example which has used this function?
>
>
>
> --
> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
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> discourse.itk.org. Please join us there!
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> Kitware offers ITK Training Courses, for more information visit:
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From srbn.ghosh99 at gmail.com  Wed May  8 02:17:02 2019
From: srbn.ghosh99 at gmail.com (Shrabani Ghosh)
Date: Tue, 7 May 2019 23:17:02 -0700 (MST)
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <CAPf2UMQjZFitRaWuP=NVFJKLuQTdKF2sBDfQj6w6kcB7eaQPOQ@mail.gmail.com>
References: <1557254060777-0.post@n2.nabble.com>
 <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
 <1557268554107-0.post@n2.nabble.com>
 <CAPf2UMQjZFitRaWuP=NVFJKLuQTdKF2sBDfQj6w6kcB7eaQPOQ@mail.gmail.com>
Message-ID: <1557296222115-0.post@n2.nabble.com>

I have tried different direction matrix collapse strategies. But still, I am
getting the same. The slices are coming out like this. 


<http://itk-insight-users.2283740.n2.nabble.com/file/t396636/slice1.png> 



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From dzenanz at gmail.com  Wed May  8 10:18:56 2019
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 8 May 2019 10:18:56 -0400
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <1557296222115-0.post@n2.nabble.com>
References: <1557254060777-0.post@n2.nabble.com>
 <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
 <1557268554107-0.post@n2.nabble.com>
 <CAPf2UMQjZFitRaWuP=NVFJKLuQTdKF2sBDfQj6w6kcB7eaQPOQ@mail.gmail.com>
 <1557296222115-0.post@n2.nabble.com>
Message-ID: <CAPf2UMQ0RMy7LpAmTm52iD6SAoMfEAtu4gUHh2K=Vm936==z9g@mail.gmail.com>

You need to use a different pixel type. You might be using char, and
needing to use unsigned char or short.

On Wed, May 8, 2019 at 2:17 AM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
wrote:

> I have tried different direction matrix collapse strategies. But still, I
> am
> getting the same. The slices are coming out like this.
>
>
> <http://itk-insight-users.2283740.n2.nabble.com/file/t396636/slice1.png>
>
>
>
> --
> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
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>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
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> Please keep messages on-topic and check the ITK FAQ at:
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From srbn.ghosh99 at gmail.com  Wed May  8 11:44:14 2019
From: srbn.ghosh99 at gmail.com (Shrabani Ghosh)
Date: Wed, 8 May 2019 11:44:14 -0400
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <CAPf2UMQ0RMy7LpAmTm52iD6SAoMfEAtu4gUHh2K=Vm936==z9g@mail.gmail.com>
References: <1557254060777-0.post@n2.nabble.com>
 <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
 <1557268554107-0.post@n2.nabble.com>
 <CAPf2UMQjZFitRaWuP=NVFJKLuQTdKF2sBDfQj6w6kcB7eaQPOQ@mail.gmail.com>
 <1557296222115-0.post@n2.nabble.com>
 <CAPf2UMQ0RMy7LpAmTm52iD6SAoMfEAtu4gUHh2K=Vm936==z9g@mail.gmail.com>
Message-ID: <CADHEK9_Yx8ytVQ=tRqfukA9AZPXV0eA6RG=if57r6jqEEE041w@mail.gmail.com>

I am using   unsigned char as output pixel and signed short as input pixel.

On Wed, May 8, 2019 at 10:19 AM D?enan Zuki? <dzenanz at gmail.com> wrote:

> You need to use a different pixel type. You might be using char, and
> needing to use unsigned char or short.
>
> On Wed, May 8, 2019 at 2:17 AM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
> wrote:
>
>> I have tried different direction matrix collapse strategies. But still, I
>> am
>> getting the same. The slices are coming out like this.
>>
>>
>> <http://itk-insight-users.2283740.n2.nabble.com/file/t396636/slice1.png>
>>
>>
>>
>> --
>> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
>> The ITK community is transitioning from this mailing list to
>> discourse.itk.org. Please join us there!
>> ________________________________
>> 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.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
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>
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From dzenanz at gmail.com  Wed May  8 11:48:45 2019
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 8 May 2019 11:48:45 -0400
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <CADHEK9_Yx8ytVQ=tRqfukA9AZPXV0eA6RG=if57r6jqEEE041w@mail.gmail.com>
References: <1557254060777-0.post@n2.nabble.com>
 <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
 <1557268554107-0.post@n2.nabble.com>
 <CAPf2UMQjZFitRaWuP=NVFJKLuQTdKF2sBDfQj6w6kcB7eaQPOQ@mail.gmail.com>
 <1557296222115-0.post@n2.nabble.com>
 <CAPf2UMQ0RMy7LpAmTm52iD6SAoMfEAtu4gUHh2K=Vm936==z9g@mail.gmail.com>
 <CADHEK9_Yx8ytVQ=tRqfukA9AZPXV0eA6RG=if57r6jqEEE041w@mail.gmail.com>
Message-ID: <CAPf2UMRfBpwshc49p6_=6hymV+eb+J72vQpwCinO1SCjd5r=OQ@mail.gmail.com>

If the input and output pixel types are different, extract filter does
simple casting. That causes the effect you have observed. You need to use
RescaleIntensityImageFilter
<https://itk.org/Doxygen/html/classitk_1_1RescaleIntensityImageFilter.html>
either
before or after the extract. Have the extract filter use the same input and
output pixel type.

On Wed, May 8, 2019 at 11:44 AM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
wrote:

> I am using   unsigned char as output pixel and signed short as input
> pixel.
>
> On Wed, May 8, 2019 at 10:19 AM D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> You need to use a different pixel type. You might be using char, and
>> needing to use unsigned char or short.
>>
>> On Wed, May 8, 2019 at 2:17 AM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
>> wrote:
>>
>>> I have tried different direction matrix collapse strategies. But still,
>>> I am
>>> getting the same. The slices are coming out like this.
>>>
>>>
>>> <http://itk-insight-users.2283740.n2.nabble.com/file/t396636/slice1.png>
>>>
>>>
>>>
>>>
>>> --
>>> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
>>> The ITK community is transitioning from this mailing list to
>>> discourse.itk.org. Please join us there!
>>> ________________________________
>>> 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.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> https://itk.org/mailman/listinfo/insight-users
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>>> discourse.itk.org. Please join us there!
>>> ________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> https://itk.org/mailman/listinfo/community
>>>
>>
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From srbn.ghosh99 at gmail.com  Wed May  8 13:54:08 2019
From: srbn.ghosh99 at gmail.com (Shrabani Ghosh)
Date: Wed, 8 May 2019 10:54:08 -0700 (MST)
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <CAPf2UMRfBpwshc49p6_=6hymV+eb+J72vQpwCinO1SCjd5r=OQ@mail.gmail.com>
References: <1557254060777-0.post@n2.nabble.com>
 <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
 <1557268554107-0.post@n2.nabble.com>
 <CAPf2UMQjZFitRaWuP=NVFJKLuQTdKF2sBDfQj6w6kcB7eaQPOQ@mail.gmail.com>
 <1557296222115-0.post@n2.nabble.com>
 <CAPf2UMQ0RMy7LpAmTm52iD6SAoMfEAtu4gUHh2K=Vm936==z9g@mail.gmail.com>
 <CADHEK9_Yx8ytVQ=tRqfukA9AZPXV0eA6RG=if57r6jqEEE041w@mail.gmail.com>
 <CAPf2UMRfBpwshc49p6_=6hymV+eb+J72vQpwCinO1SCjd5r=OQ@mail.gmail.com>
Message-ID: <1557338048860-0.post@n2.nabble.com>

I did it like this and I am getting images like this now. 
<http://itk-insight-users.2283740.n2.nabble.com/file/t396636/slice1.png> 



int main( int argc, char ** argv )
{
  
  //typedef signed short        InputPixelType;
  /*typedef unsigned char       InputPixelType;
  typedef unsigned char        OutputPixelType;*/
  typedef signed short       InputPixelType;
  typedef unsigned char      OutputPixelType;
  typedef itk::Image< InputPixelType,  3 >    InputImageType;
  typedef itk::Image< OutputPixelType, 2 >    OutputImageType;
  typedef itk::ImageFileReader< InputImageType  >  ReaderType;
  typedef itk::ImageFileWriter< OutputImageType >  WriterType;
  const char * inputFilename  = "G:/My Drive/BMES2019/New
folder/subject1.nii";

  {
	        int i = 1;
  
			std::string str="input//";
			std::string s1="slice";
			std::string s2 = std::to_string(i);
			std::string s3=".png";
			std::string s4=str+s1+s2+s3;
			const char *mycharp = s4.c_str();
	
  const char * outputFilename = mycharp;

  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();

  reader->SetFileName( inputFilename  );
  writer->SetFileName( outputFilename );

   typedef itk::RescaleIntensityImageFilter< InputImageType, InputImageType
> RescaleFilterType;
   RescaleFilterType::Pointer rescalefilter = RescaleFilterType::New();
   rescalefilter->SetInput( reader->GetOutput() );

  typedef itk::ExtractImageFilter< InputImageType,
                                   OutputImageType > FilterType;
  FilterType::Pointer filter = FilterType::New();
  filter->InPlaceOn();
  filter->SetDirectionCollapseToSubmatrix();
   reader->UpdateOutputInformation();
  InputImageType::RegionType inputRegion =
           reader->GetOutput()->GetLargestPossibleRegion();

  InputImageType::SizeType size = inputRegion.GetSize();
  size[2] = 0;

  InputImageType::IndexType start = inputRegion.GetIndex();
  const unsigned int sliceNumber = stoi(s2);//atoi(argv[3]);
  start[2] = sliceNumber;

  InputImageType::RegionType desiredRegion;
  desiredRegion.SetSize(  size  );
  desiredRegion.SetIndex( start );

  filter->SetExtractionRegion( desiredRegion );

  filter->SetInput( rescalefilter->GetOutput() );
  writer->SetInput( filter->GetOutput() );
   try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & err )
    {
    std::cerr << "ExceptionObject caught !" << std::endl;
    std::cerr << err << std::endl;
	getchar();
    return EXIT_FAILURE;
    }
    }
  return EXIT_SUCCESS;
}



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From dzenanz at gmail.com  Wed May  8 14:17:20 2019
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 8 May 2019 14:17:20 -0400
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <1557338048860-0.post@n2.nabble.com>
References: <1557254060777-0.post@n2.nabble.com>
 <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
 <1557268554107-0.post@n2.nabble.com>
 <CAPf2UMQjZFitRaWuP=NVFJKLuQTdKF2sBDfQj6w6kcB7eaQPOQ@mail.gmail.com>
 <1557296222115-0.post@n2.nabble.com>
 <CAPf2UMQ0RMy7LpAmTm52iD6SAoMfEAtu4gUHh2K=Vm936==z9g@mail.gmail.com>
 <CADHEK9_Yx8ytVQ=tRqfukA9AZPXV0eA6RG=if57r6jqEEE041w@mail.gmail.com>
 <CAPf2UMRfBpwshc49p6_=6hymV+eb+J72vQpwCinO1SCjd5r=OQ@mail.gmail.com>
 <1557338048860-0.post@n2.nabble.com>
Message-ID: <CAPf2UMThLrzFJ1JQJMqgBa1Ks2P1+jkG5K=kBhfduJoVsv46cA@mail.gmail.com>

Definitions of RescaleFilterType and FilterType should be like this:

typedef itk::RescaleIntensityImageFilter< InputImageType, OutputImageType >
RescaleFilterType;
typedef itk::ExtractImageFilter< OutputImageType, OutputImageType >
FilterType;

On Wed, May 8, 2019 at 1:54 PM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
wrote:

> I did it like this and I am getting images like this now.
> <http://itk-insight-users.2283740.n2.nabble.com/file/t396636/slice1.png>
>
>
>
> int main( int argc, char ** argv )
> {
>
>   //typedef signed short        InputPixelType;
>   /*typedef unsigned char       InputPixelType;
>   typedef unsigned char        OutputPixelType;*/
>   typedef signed short       InputPixelType;
>   typedef unsigned char      OutputPixelType;
>   typedef itk::Image< InputPixelType,  3 >    InputImageType;
>   typedef itk::Image< OutputPixelType, 2 >    OutputImageType;
>   typedef itk::ImageFileReader< InputImageType  >  ReaderType;
>   typedef itk::ImageFileWriter< OutputImageType >  WriterType;
>   const char * inputFilename  = "G:/My Drive/BMES2019/New
> folder/subject1.nii";
>
>   {
>                 int i = 1;
>
>                         std::string str="input//";
>                         std::string s1="slice";
>                         std::string s2 = std::to_string(i);
>                         std::string s3=".png";
>                         std::string s4=str+s1+s2+s3;
>                         const char *mycharp = s4.c_str();
>
>   const char * outputFilename = mycharp;
>
>   ReaderType::Pointer reader = ReaderType::New();
>   WriterType::Pointer writer = WriterType::New();
>
>   reader->SetFileName( inputFilename  );
>   writer->SetFileName( outputFilename );
>
>    typedef itk::RescaleIntensityImageFilter< InputImageType, InputImageType
> > RescaleFilterType;
>    RescaleFilterType::Pointer rescalefilter = RescaleFilterType::New();
>    rescalefilter->SetInput( reader->GetOutput() );
>
>   typedef itk::ExtractImageFilter< InputImageType,
>                                    OutputImageType > FilterType;
>   FilterType::Pointer filter = FilterType::New();
>   filter->InPlaceOn();
>   filter->SetDirectionCollapseToSubmatrix();
>    reader->UpdateOutputInformation();
>   InputImageType::RegionType inputRegion =
>            reader->GetOutput()->GetLargestPossibleRegion();
>
>   InputImageType::SizeType size = inputRegion.GetSize();
>   size[2] = 0;
>
>   InputImageType::IndexType start = inputRegion.GetIndex();
>   const unsigned int sliceNumber = stoi(s2);//atoi(argv[3]);
>   start[2] = sliceNumber;
>
>   InputImageType::RegionType desiredRegion;
>   desiredRegion.SetSize(  size  );
>   desiredRegion.SetIndex( start );
>
>   filter->SetExtractionRegion( desiredRegion );
>
>   filter->SetInput( rescalefilter->GetOutput() );
>   writer->SetInput( filter->GetOutput() );
>    try
>     {
>     writer->Update();
>     }
>   catch( itk::ExceptionObject & err )
>     {
>     std::cerr << "ExceptionObject caught !" << std::endl;
>     std::cerr << err << std::endl;
>         getchar();
>     return EXIT_FAILURE;
>     }
>     }
>   return EXIT_SUCCESS;
> }
>
>
>
> --
> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> 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.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> https://itk.org/mailman/listinfo/insight-users
>
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From srbn.ghosh99 at gmail.com  Wed May  8 20:13:00 2019
From: srbn.ghosh99 at gmail.com (Shrabani Ghosh)
Date: Wed, 8 May 2019 17:13:00 -0700 (MST)
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <CAPf2UMThLrzFJ1JQJMqgBa1Ks2P1+jkG5K=kBhfduJoVsv46cA@mail.gmail.com>
References: <1557254060777-0.post@n2.nabble.com>
 <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
 <1557268554107-0.post@n2.nabble.com>
 <CAPf2UMQjZFitRaWuP=NVFJKLuQTdKF2sBDfQj6w6kcB7eaQPOQ@mail.gmail.com>
 <1557296222115-0.post@n2.nabble.com>
 <CAPf2UMQ0RMy7LpAmTm52iD6SAoMfEAtu4gUHh2K=Vm936==z9g@mail.gmail.com>
 <CADHEK9_Yx8ytVQ=tRqfukA9AZPXV0eA6RG=if57r6jqEEE041w@mail.gmail.com>
 <CAPf2UMRfBpwshc49p6_=6hymV+eb+J72vQpwCinO1SCjd5r=OQ@mail.gmail.com>
 <1557338048860-0.post@n2.nabble.com>
 <CAPf2UMThLrzFJ1JQJMqgBa1Ks2P1+jkG5K=kBhfduJoVsv46cA@mail.gmail.com>
Message-ID: <1557360780373-0.post@n2.nabble.com>

I tried based on your recommendation. But still could not make it. Any other
suggestions?







--
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The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
________________________________
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.php

Please keep messages on-topic and check the ITK FAQ at:
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Follow this link to subscribe/unsubscribe:
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From dzenanz at gmail.com  Thu May  9 08:29:27 2019
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 9 May 2019 08:29:27 -0400
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <1557360780373-0.post@n2.nabble.com>
References: <1557254060777-0.post@n2.nabble.com>
 <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
 <1557268554107-0.post@n2.nabble.com>
 <CAPf2UMQjZFitRaWuP=NVFJKLuQTdKF2sBDfQj6w6kcB7eaQPOQ@mail.gmail.com>
 <1557296222115-0.post@n2.nabble.com>
 <CAPf2UMQ0RMy7LpAmTm52iD6SAoMfEAtu4gUHh2K=Vm936==z9g@mail.gmail.com>
 <CADHEK9_Yx8ytVQ=tRqfukA9AZPXV0eA6RG=if57r6jqEEE041w@mail.gmail.com>
 <CAPf2UMRfBpwshc49p6_=6hymV+eb+J72vQpwCinO1SCjd5r=OQ@mail.gmail.com>
 <1557338048860-0.post@n2.nabble.com>
 <CAPf2UMThLrzFJ1JQJMqgBa1Ks2P1+jkG5K=kBhfduJoVsv46cA@mail.gmail.com>
 <1557360780373-0.post@n2.nabble.com>
Message-ID: <CAPf2UMQJ77vaOtrcR+Us7rUsQe1SFEVpjsD701r7JL0t76pvZw@mail.gmail.com>

How does the output look like now?

On Wed, May 8, 2019 at 8:13 PM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
wrote:

> I tried based on your recommendation. But still could not make it. Any
> other
> suggestions?
>
>
>
>
>
>
>
> --
> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> 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.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> https://itk.org/mailman/listinfo/insight-users
>
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Visit other Kitware open-source projects at
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Please keep messages on-topic and check the ITK FAQ at:
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Follow this link to subscribe/unsubscribe:
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From srbn.ghosh99 at gmail.com  Thu May  9 12:49:03 2019
From: srbn.ghosh99 at gmail.com (Shrabani Ghosh)
Date: Thu, 9 May 2019 12:49:03 -0400
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <CAPf2UMQJ77vaOtrcR+Us7rUsQe1SFEVpjsD701r7JL0t76pvZw@mail.gmail.com>
References: <1557254060777-0.post@n2.nabble.com>
 <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
 <1557268554107-0.post@n2.nabble.com>
 <CAPf2UMQjZFitRaWuP=NVFJKLuQTdKF2sBDfQj6w6kcB7eaQPOQ@mail.gmail.com>
 <1557296222115-0.post@n2.nabble.com>
 <CAPf2UMQ0RMy7LpAmTm52iD6SAoMfEAtu4gUHh2K=Vm936==z9g@mail.gmail.com>
 <CADHEK9_Yx8ytVQ=tRqfukA9AZPXV0eA6RG=if57r6jqEEE041w@mail.gmail.com>
 <CAPf2UMRfBpwshc49p6_=6hymV+eb+J72vQpwCinO1SCjd5r=OQ@mail.gmail.com>
 <1557338048860-0.post@n2.nabble.com>
 <CAPf2UMThLrzFJ1JQJMqgBa1Ks2P1+jkG5K=kBhfduJoVsv46cA@mail.gmail.com>
 <1557360780373-0.post@n2.nabble.com>
 <CAPf2UMQJ77vaOtrcR+Us7rUsQe1SFEVpjsD701r7JL0t76pvZw@mail.gmail.com>
Message-ID: <CADHEK99ZMpc3tJgc_oJBrOe+NL8GYNt3Vd54E6BG7w_x6P90Ww@mail.gmail.com>

It's the same in the beginning I got.

On Thu, May 9, 2019 at 8:29 AM D?enan Zuki? <dzenanz at gmail.com> wrote:

> How does the output look like now?
>
> On Wed, May 8, 2019 at 8:13 PM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
> wrote:
>
>> I tried based on your recommendation. But still could not make it. Any
>> other
>> suggestions?
>>
>>
>>
>>
>>
>>
>>
>> --
>> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
>> The ITK community is transitioning from this mailing list to
>> discourse.itk.org. Please join us there!
>> ________________________________
>> 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.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> https://itk.org/mailman/listinfo/insight-users
>>
>
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From dzenanz at gmail.com  Thu May  9 12:52:41 2019
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 9 May 2019 12:52:41 -0400
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <CADHEK99ZMpc3tJgc_oJBrOe+NL8GYNt3Vd54E6BG7w_x6P90Ww@mail.gmail.com>
References: <1557254060777-0.post@n2.nabble.com>
 <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
 <1557268554107-0.post@n2.nabble.com>
 <CAPf2UMQjZFitRaWuP=NVFJKLuQTdKF2sBDfQj6w6kcB7eaQPOQ@mail.gmail.com>
 <1557296222115-0.post@n2.nabble.com>
 <CAPf2UMQ0RMy7LpAmTm52iD6SAoMfEAtu4gUHh2K=Vm936==z9g@mail.gmail.com>
 <CADHEK9_Yx8ytVQ=tRqfukA9AZPXV0eA6RG=if57r6jqEEE041w@mail.gmail.com>
 <CAPf2UMRfBpwshc49p6_=6hymV+eb+J72vQpwCinO1SCjd5r=OQ@mail.gmail.com>
 <1557338048860-0.post@n2.nabble.com>
 <CAPf2UMThLrzFJ1JQJMqgBa1Ks2P1+jkG5K=kBhfduJoVsv46cA@mail.gmail.com>
 <1557360780373-0.post@n2.nabble.com>
 <CAPf2UMQJ77vaOtrcR+Us7rUsQe1SFEVpjsD701r7JL0t76pvZw@mail.gmail.com>
 <CADHEK99ZMpc3tJgc_oJBrOe+NL8GYNt3Vd54E6BG7w_x6P90Ww@mail.gmail.com>
Message-ID: <CAPf2UMTxQwehRhXmF5+r5nh=fpob=aKi4nk_J--ZiCWq0TMK0g@mail.gmail.com>

Please post this question to the forum <https://discourse.itk.org/>.
Include the current source code and the output image. If possible, also
include a crop or screenshot of the input image.

Regards,
D?enan

On Thu, May 9, 2019 at 12:49 PM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
wrote:

> It's the same in the beginning I got.
>
> On Thu, May 9, 2019 at 8:29 AM D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> How does the output look like now?
>>
>> On Wed, May 8, 2019 at 8:13 PM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
>> wrote:
>>
>>> I tried based on your recommendation. But still could not make it. Any
>>> other
>>> suggestions?
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
>>> The ITK community is transitioning from this mailing list to
>>> discourse.itk.org. Please join us there!
>>> ________________________________
>>> 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.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> https://itk.org/mailman/listinfo/insight-users
>>>
>>
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From srbn.ghosh99 at gmail.com  Thu May  9 13:48:00 2019
From: srbn.ghosh99 at gmail.com (Shrabani Ghosh)
Date: Thu, 9 May 2019 13:48:00 -0400
Subject: [ITK] [ITK-users] Image conversion from 3D volume to 2D slices
In-Reply-To: <CAPf2UMTxQwehRhXmF5+r5nh=fpob=aKi4nk_J--ZiCWq0TMK0g@mail.gmail.com>
References: <1557254060777-0.post@n2.nabble.com>
 <CAPf2UMSYdJqhPO-8d2Ejn75_CmV3GWRVtvpfqXnTLchPyWCwMg@mail.gmail.com>
 <1557268554107-0.post@n2.nabble.com>
 <CAPf2UMQjZFitRaWuP=NVFJKLuQTdKF2sBDfQj6w6kcB7eaQPOQ@mail.gmail.com>
 <1557296222115-0.post@n2.nabble.com>
 <CAPf2UMQ0RMy7LpAmTm52iD6SAoMfEAtu4gUHh2K=Vm936==z9g@mail.gmail.com>
 <CADHEK9_Yx8ytVQ=tRqfukA9AZPXV0eA6RG=if57r6jqEEE041w@mail.gmail.com>
 <CAPf2UMRfBpwshc49p6_=6hymV+eb+J72vQpwCinO1SCjd5r=OQ@mail.gmail.com>
 <1557338048860-0.post@n2.nabble.com>
 <CAPf2UMThLrzFJ1JQJMqgBa1Ks2P1+jkG5K=kBhfduJoVsv46cA@mail.gmail.com>
 <1557360780373-0.post@n2.nabble.com>
 <CAPf2UMQJ77vaOtrcR+Us7rUsQe1SFEVpjsD701r7JL0t76pvZw@mail.gmail.com>
 <CADHEK99ZMpc3tJgc_oJBrOe+NL8GYNt3Vd54E6BG7w_x6P90Ww@mail.gmail.com>
 <CAPf2UMTxQwehRhXmF5+r5nh=fpob=aKi4nk_J--ZiCWq0TMK0g@mail.gmail.com>
Message-ID: <CADHEK9-+dut=3HDJ+A=1XbemhP1BeHmMNqd0SJn23RiM=zw4gw@mail.gmail.com>

Okay, Thank you. I have posted there,



On Thu, May 9, 2019 at 12:52 PM D?enan Zuki? <dzenanz at gmail.com> wrote:

> Please post this question to the forum <https://discourse.itk.org/>.
> Include the current source code and the output image. If possible, also
> include a crop or screenshot of the input image.
>
> Regards,
> D?enan
>
> On Thu, May 9, 2019 at 12:49 PM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
> wrote:
>
>> It's the same in the beginning I got.
>>
>> On Thu, May 9, 2019 at 8:29 AM D?enan Zuki? <dzenanz at gmail.com> wrote:
>>
>>> How does the output look like now?
>>>
>>> On Wed, May 8, 2019 at 8:13 PM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
>>> wrote:
>>>
>>>> I tried based on your recommendation. But still could not make it. Any
>>>> other
>>>> suggestions?
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
>>>> The ITK community is transitioning from this mailing list to
>>>> discourse.itk.org. Please join us there!
>>>> ________________________________
>>>> 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.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> https://itk.org/mailman/listinfo/insight-users
>>>>
>>>
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From ee18d504 at iittp.ac.in  Fri May 24 06:31:10 2019
From: ee18d504 at iittp.ac.in (EE18D504 SINDHURA C)
Date: Fri, 24 May 2019 16:01:10 +0530
Subject: [ITK] [ITK-users] Registration - How to save deformation field.?
Message-ID: <CAAssdXo-opx1d3vFYRp3dRhVvCz-g+phVOetri+03PKffRsaUw@mail.gmail.com>

Hi
 I am executing deformableregistration15.cxx file. I wonder how to save the
deformation field? In which format should I save it? I tried mha and mhd
format. But it throws an error message.


Regards
Sindhu
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