[Insight-users] Read mnc files
Prename Surname
bsd.diverse at gmail.com
Tue Oct 3 03:17:03 EDT 2006
Hmmm but since there has been built an minc-reader, it should be possible to
read and use .mnc files in ITK.
Otherwise Mrs. Leila Baghdadi has wasted some time...
Thank you for the advice though, but I would really hope that i can avoid to
convert between different fileformats, as this introduces an extra layer
which should'nt be necessary.
Did anyone experience a problem like the one i am having with the
H5public.h.
where i get the error :
error C2632: 'int' followed by 'ini' is illegal (Line: 122)
Best of regards
2006/10/3, Richard Beare <richard.beare at gmail.com>:
>
> If you have successfully built the associated minc libraries that are
> distributed with mincio you should have access to a tool called
> mnc2nii, which lets you convert minc to nifti or analyze. Both nifti
> and analyze are supported by ITK so you should be able to read the
> data without any messing around.
>
> I haven't done this under windows though.
>
> On 10/3/06, Prename Surname <bsd.diverse at gmail.com> wrote:
> > Sorry, I said somethin wrong. I´used this CMakeLists.txt to build my
> visual
> > studio project:
> >
> >
> > PROJECT(Hello)
> >
> > SET(HFILES
> > "D:\\skole\\imaging_software\\itk\\src\\Code\\IO"
> > "D:\\skole\\imaging_software\\itk\\src\\Code\\Common"
> >
> > "D:\\skole\\imaging_software\\itk\\src\\Code\\BasicFilters"
> > "C:\\Program Files\\MNI\\MINC\\include"
> > )
> >
> >
> > FIND_PACKAGE(ITK)
> > IF (ITK_FOUND)
> > INCLUDE(${USE_ITK_FILE})
> > ENDIF(ITK_FOUND)
> >
> > FIND_PACKAGE(VTK)
> > IF(VTK_FOUND)
> > INCLUDE( ${USE_VTK_FILE} )
> > ENDIF(VTK_FOUND)
> >
> > INCLUDE_DIRECTORIES(
> > ${Hello_SOURCE_DIR}
> > ${HFILES}
> > )
> > ADD_EXECUTABLE(Hello main.cxx)
> > TARGET_LINK_LIBRARIES (Hello
> > ITKBasicFilters ITKCommon ITKIO
> > vtkRendering vtkGraphics vtkHybrid
> > vtkImaging vtkIO vtkFiltering vtkCommon
> > )
> >
> >
> >
> >
> > It could be that i am missing something essential?
> >
> > I really look forward to hearing for you. Many regards
> >
> >
> >
> > 2006/10/2, Prename Surname <bsd.diverse at gmail.com>:
> > >
> > > Hello again
> > >
> > > I have downloaded the mincreader, and done everything as mentioned in
> the
> > README file, meaning moved the CMakeLists.txt files, moved the .cxx
> files
> > etc. and rerun cmake to build itk again.
> > >
> > > That went without problems. I do however get a problem when i want to
> > build the testprogram for testing the mincfiles. I am running on windows
> XP,
> > and using Visual Studio 8(2005).
> > > When i have run cmake on the
> > Insight_Testing_Code_IO_CMakeLists.txt (of course renamed)
> > > and created the visual studio project and press BUILD ALL project, to
> > build i get an error in a header file called H5public.h. I think this
> file
> > belongs to the hdf5 package.
> > >
> > > The error i get is the following:
> > > error C2632: 'int' followed by 'ini' is illegal (Line: 122)
> > >
> > > I did not change any of that code at all, so there must be something
> wrong
> > with a compiler flag i am missing or something else.
> > > I am quite lost here. I really hope someone can help me on this. Many
> > regards
> > >
> > >
> > > 2006/9/30, Vincent Magnotta <vincent-magnotta at uiowa.edu>:
> > >
> > > > Prename,
> > > >
> > > > It is possible to do this in ITK. It may be easier however to get
> > > > started by running the mincextract program on the slices to build up
> a
> > > > raw volume of data. You could then create a meta image header for
> the
> > > > volume.
> > > >
> > > > To do this directly in ITK you would want to use something like the
> > > > PasteImageFilter.
> > > >
> > > > Vince
> > > >
> > > >
> > > > Prename Surname wrote:
> > > >
> > > > > Yeah, this seems to work :)
> > > > > Thank you very much. I will try it out and ill return with some
> > feedback.
> > > > >
> > > > > Best of regards.
> > > > >
> > > > > Do you know what function i should use if i want to make a volume
> out
> > > > > of my slices?
> > > > >
> > > > >
> > > > > 2006/9/30, Vincent Magnotta <vincent-magnotta at uiowa.edu
> > > > > <mailto:vincent-magnotta at uiowa.edu >>:
> > > > >
> > > > > Prename,
> > > > >
> > > > > That is odd. It works for me. Anyway give this link a try.
> > > > >
> > > > > *|http://hdl.handle.net/1926/191
> > > > >
> > > > > Vince
> > > > >
> > > > > |*
> > > > > Prename Surname wrote:
> > > > >
> > > > > > Ahhh this sounds very interresting indeed.
> > > > > > But the link seems to be dead. is there some spelling error?
> > > > > >
> > > > > > Regards
> > > > > >
> > > > > >
> > > > > > 2006/9/29, Vincent Magnotta < vincent-magnotta at uiowa.edu
> > > > > <mailto: vincent-magnotta at uiowa.edu>
> > > > > > <mailto: vincent-magnotta at uiowa.edu
> > > > > <mailto: vincent-magnotta at uiowa.edu >>>:
> > > > > >
> > > > > > Prename,
> > > > > >
> > > > > > ITK currently does not support MINC files directly. A
> MINC
> > > > > 2.0 reader
> > > > > > was submitted to the Insight Journal
> > > > > >
> > (http://insight-journal.org/dspace/handle/1926/191) by
> > Leila
> > > > > > Baghdadi to
> > > > > > read this files into ITK. You will want to download this
> > > > > code and
> > > > > > see if
> > > > > > this allows you to read in the data. You are also
> encouraged
> > to
> > > > > > provide
> > > > > > a review of the software in the Insight Journal once you
> > have
> > > > > > downloaded
> > > > > > and tested the software.
> > > > > >
> > > > > > Vince
> > > > > >
> > > > > >
> > > > > > Prename Surname wrote:
> > > > > >
> > > > > > > Hello.
> > > > > > > I have brainslices taken in an MR-scanner.
> > > > > > > My first goal is to create a 3D image of all the
> slices,
> > but
> > > > > > before i
> > > > > > > can do that i need to be able to read them with
> itk/vtk
> > first.
> > > > > > > As of now they are saved in the format .mnc, which i
> was
> > > > > really
> > > > > > hoping
> > > > > > > itk/vtk can read.
> > > > > > > So my question is, how do i read .mnc images with
> itk/vtk,
> > > > > and if it
> > > > > > > cannot, then what format should i then convert them to
> > > > > instead?
> > > > > > >
> > > > > > > Many regards.
> > > > > > >
> > > > > > > P.S. Is it difficult to create a 3D model of my
> slices?
> > > > > > >
> > > > > >
> > > > >
> >
> >------------------------------------------------------------------------
> > > > >
> > > > > > >
> > > > > >
> > >_______________________________________________
> > > > > > >Insight-users mailing list
> > > > > > >Insight-users at itk.org <mailto: Insight-users at itk.org>
> > > > > <mailto: Insight-users at itk.org <mailto: Insight-users at itk.org>>
> > > > > >
> > >http://www.itk.org/mailman/listinfo/insight-users
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Assistant Professor
> > > > > > Department of Radiology
> > > > > > 0453-D JCP
> > > > > > 200 Hawkins Drive
> > > > > > Iowa City, IA 52242
> > > > > > E-mail: vincent-magnotta at uiowa.edu
> > > > > <mailto:vincent-magnotta at uiowa.edu>
> > > > > <mailto: vincent-magnotta at uiowa.edu
> > > > > <mailto: vincent-magnotta at uiowa.edu>>
> > > > > > Phone: 319-356-8255
> > > > > > Fax: 319-353-6275
> > > > > > Website: http://www.radiology.uiowa.edu
> > > > > <http://www.radiology.uiowa.edu >
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Assistant Professor
> > > > > Department of Radiology
> > > > > 0453-D JCP
> > > > > 200 Hawkins Drive
> > > > > Iowa City, IA 52242
> > > > > E-mail: vincent-magnotta at uiowa.edu
> > <mailto:vincent-magnotta at uiowa.edu>
> > > > > Phone: 319-356-8255
> > > > > Fax: 319-353-6275
> > > > > Website: http://www.radiology.uiowa.edu
> > > > >
> > > > >
> > > >
> > > >
> > > > --
> > > > Assistant Professor
> > > > Department of Radiology
> > > > 0453-D JCP
> > > > 200 Hawkins Drive
> > > > Iowa City, IA 52242
> > > > E-mail: vincent-magnotta at uiowa.edu
> > > > Phone: 319-356-8255
> > > > Fax: 319-353-6275
> > > > Website: http://www.radiology.uiowa.edu
> > > >
> > > >
> > >
> > >
> >
> >
> > _______________________________________________
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> > Insight-users at itk.org
> > http://www.itk.org/mailman/listinfo/insight-users
> >
> >
> >
>
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