[Insight-users] Reading 3D Binary Volumes

[Luis Ibanez]

Hi Aya,

The simplest way of loading a "raw" binary file into ITK is
to write a MetaImage header for it.

This is simply a text header file, that you will put in the same
directory as your binary file.

As described in:
http://www.itk.org/ITK/resources/links.html

The minimal MetaImage header would be a file with extension
".mhd", named for example:

                             "image.mhd"

with content such as:

NDims = 3
DimSize = 181 217 181
ElementType = MET_UCHAR
ElementSpacing = 1.2 1.2 3.4
Offset = 13.4 27.5 43.2
ElementByteOrderMSB = False
ElementDataFile = myBinaryFile.raw


Where, of course, you will have to replace the
"myBinaryFile.raw" with the actual filename of
your binary file.

The DimSize field with the actual number of pixels
along each dimension of your image.

The ElementType with the pixel type of the data.
Presumably you are doing CT or MRI, and in that
case you want to use the pixel type MET_SHORT.

Offset should have the coordinates of the image
origin.

All that said,
Please note that you could could have just read
the DICOM image directly into ITK, as explained
in the ITK Software Guide

      http://www.itk.org/ItkSoftwareGuide.pdf

in the "Reading and Writing Images" Chapter.

You will find source code examples on how to
read DICOM  images in the directory:

            Insight/Examples/IO


The other options that you mention are also valid.

You could read the image as DICOM and save it
as a .vtk legacy file (although in this case the
direction cosines will be lost... but you already
lost them anyways in your current process of
saving only the binary data).

You could also save the image as an Analyze
or Nifti image file format. But please note that
Analyze only supports three image orientations.

My suggestion will be to save the image using
the MetaImage file format, or to keep it as a
DICOM file.  Those are the two options that
will keep the largest amount of information about
your image.


    Regards,


           Luis

------------------------------------------------------------------------------
On Thu, Oct 22, 2009 at 10:26 AM, Aya El Gebeely
<aya.elgebeely at symbyo.com> wrote:
> Dear Luis,
>
...
>
> I 've a question concerning  reading 3D images & applying ITK filters on 3D
> images.
>
> I have 3D volumes that were constructed from DICOM series & were saved in
> Binary Files. [the pixel data]
>
> Here is the issue :
>
> I need to reconstruct the volume, and apply some ITK filters on it such as
> segmentation, Diluting, Laplacian and others
>
> I'm facing a problem in reading the binary file using ItkImageReader, it
> fails to load pixel data.
>
> - Should I use another kind of reader with the binary volume ?
> - Should I stop using binary file and save the volume in another format ?
>
> What is your opinion about this problem ?
>
> Thanks in advance and waiting for your reply :)
>
> Best Regards,
> Aya R. ElGebeely
> Software Engineer
> Symbyo Technologies
>