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

[David Gobbi]

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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