[vtkusers] vtkNIFTIImageReader.h: No such file or directory

[Francisco Lopez de la Franca]

Hi again.
I've already got the convex hull of my Nifti image, and you were right
regarding the output image file. I'm saving in VTP format.
I have another question.
When I read the Nifti image, I also store its spacing, origin and dimension.
When displaying the VTP file in 3D Slicer, the convex hull is shifted
compared with the original image. How can I do to preserve the original
origin and dimension? Neither the vtkImageMarchingCubes nor vtkHull contain
the suited methods.
I hope the question is clear and makes sense.
Thanks a lot.
MBR.
/Francisco


2015-05-25 14:48 GMT+02:00 David Gobbi <david.gobbi at gmail.com>:

> Hi Francisco,
>
> The vtkHull and vtkDelaunay3D classes require vtkPolyData as input. I
> suspect that you need vtkImageMarchingCubes or vtkContourFilter.
>
> However, the output of these filters cannot be written to a NIFTI file.
> In fact, I'm a bit confused when you say "write a convex hull to a NIFTI
> file".  A convex hull is a geometrical surface (e.g. made of polygons), but
> NIFTI is an image file format.
>
>  - David
>
> On Mon, May 25, 2015 at 6:35 AM, Francisco Lopez de la Franca <
> franciscolopezdelafranca at gmail.com> wrote:
>
>> Hi.
>> Thanks a lot. I've just downloaded VTK 6.2.0 and I've realised that there
>> it is what I need.
>> But, I take advantage of this moment to tell about another problem.
>>
>> I read a NIFTI file (abc.nii) through vtkNIFTIImageReader. Its output is
>> passed to either vtkHull or vtkDelaunay3D in order to get the convex hull
>> of the objects in the Nifti image.
>>
>> And, in the end, I write their result with vtkNIFTIImageWriter.
>>
>> The compilation goes right, but the execution (on a Windows system) does
>> not produce anything and I hardly see a "command prompt" window flashing
>> only once, but I am unable to read its content.
>>
>> I think there must be some incompatibility between the output of
>> vtkNifitiImageReader and the input to vtkHull or vtkDelaunay3D, or
>> something similar.
>>
>> Any suggestion on how to read a NIFTI file and get its convex hull and
>> then write it to another Nifti file.
>>
>> Thank you very much.
>> /Francisco
>>
>> 2015-05-25 14:25 GMT+02:00 David Gobbi <david.gobbi at gmail.com>:
>>
>>> Hi Francisco,
>>>
>>> The vtkNIFTIImageReader did not appear until VTK 6.2.
>>> There are two options that I can recommend:
>>>
>>> 1) Use the VTK git master, which has the most recent update to the NIFTI
>>> reader (the vtkNIFTIImageReader in VTK 6.2 gives the wrong sform offset in
>>> some situations, this is fixed in git master).
>>>
>>> 2) If you want to keep the VTK you have, then you can get the NIFTI
>>> reader separately by building the vtk-dicom package:
>>> https://github.com/dgobbi/vtk-dicom (the class is called
>>> "vtkNIFTIReader" in vtk-dicom, but is otherwise identical to the one in the
>>> VTK git master branch).
>>>
>>> Cheers,
>>>  - David
>>>
>>>
>>>
>>> On Mon, May 25, 2015 at 1:54 AM, Francisco Lopez de la Franca <
>>> franciscolopezdelafranca at gmail.com> wrote:
>>>
>>>> Hi everybody.
>>>> I'd like to read a NIFTI image from VTK.
>>>> I downloaded and compiled VTK 6.1.0, but when I include the
>>>> vtkNIFTIImageReader header file, the compilation gives the error "No such
>>>> file or directory".
>>>> I've searched for the header file into the VTK directory and it is
>>>> true, there is no such a file.
>>>>
>>>> I've tested with vtkImageReader2 and compilation goes fine, but the
>>>> NIFTI file read does not seem to go well.
>>>>
>>>> Does anybody know what the problem could be?
>>>>
>>>> Thanks a lot.
>>>> My best regards.
>>>> /Francisco
>>>>
>>>> P.D.: My CMakeLists.txt contains the next lines:
>>>>
>>>> cmake_minimum_required(VERSION 2.8)
>>>>
>>>> project(CV_TFM_CONVEX_HULL)
>>>>
>>>> # Find VTK.
>>>> find_package(VTK REQUIRED)
>>>> include(${VTK_USE_FILE})
>>>>
>>>> set(CV_TFM_CONVEX_HULL_SRC CV_TFM_ConvexHull.cxx)
>>>>
>>>> add_executable(CV_TFM_CONVEX_HULL ${CV_TFM_CONVEX_HULL_SRC})
>>>>
>>>> target_link_libraries(CV_TFM_CONVEX_HULL ${VTK_LIBRARIES})
>>>>
>>>>
>>>
>>
>
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