[Insight-users] Read mnc files
Richard Beare
richard.beare at gmail.com
Mon Oct 2 21:01:20 EDT 2006
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?
> > > > > >
> > > > >
> > > >
> >------------------------------------------------------------------------
> > > >
> > > > > >
> > > > >
> >_______________________________________________
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> > > > <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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