[Insight-users] load a CT scan (DICOM)

[Alberto Bert]

Hi,

any news about your program for generate 3D MetaImages from a directory
of dicom files?

I worked on other parts of my program and now I'm facing again the
3D-DICOM from 2D-stack problem.

Thanks for your patience,
Alberto

On set 13 at 12:49-0400, Stephen R. Aylward wrote:
> Hi,
> 
> The answer may be simple...Sometimes dicom transfers occur in order - so 
> the file numbers actually correspond (by luck) to how the slices should 
> be ordered to create a 3D volume.
> 
> In that case, you can use the MetaImage format to read the dicom slices 
> to create a volume.   You can use the Insight/Example/MetaImageImporter 
> to walk you thru the process to create a MetaImage header file that will 
> allow the slices to be loaded.   Or you can write the MetaImage header 
> file yourself.   The MetaImage header format is simple and will resemble
> 
> NDims = 3
> DimSize = 512 512 <Enter#OfSlicesHere>
> ElementSpacing = <EnterXPointSize> <EnterYPointSize> <EnterSliceSpacing>
> HeaderSize = -1
> ElementType = MET_USHORT
> ElementByteOrderMSB = True
> ElementDataFile = LIST
> <EnterFileNameOfFirstSlice>
> <EnterFileNameOFSecondSlice>
> <EnterFileNameOfThirdSlice>
> .
> .
> .
> 
> 
> This is assuming the slices are 512x512 (most CT scans) of Unsigned 
> Shorts (valid for most CT dicom), and the Byte Ordering is MSB (the 
> default for most dicom).   By setting HeaderSize = -1 the program will 
> automatically calculate the header size for each slice under the 
> assumption that the pixel data occurs at the end of each slice's file 
> (which is generally true for dicom).
> 
> HOWEVER, DICOM does not guarantee order of delivery of slices - so, the 
> file numbering might be absolutely unrelated to how the slices should be 
> ordered to create a 3D volume.   You can try to figure out the ordering, 
> but that is really tedious.   Otherwise, we are working on a program to 
> automatically generate 3D MetaImages from a directory of dicom files. 
> It may be a few weeks before that program is ready.
> 
> I hope this helps,
> Stephen
> 
> Alberto Bert wrote:
> >Hi all,
> >
> >I'm interested in loading a CT (comput. tomography) scan in itk.
> >I know that DicomImageIO can get DICOM file (medical images standard
> >format), but in this case each slice (2D images at specified z, forming
> >the 3D image when in stak) is in a separate file. I mean, I would like
> >to read several 2D DICOM files (each containing a slice) and organizing
> >them to form a 3D image for itk.
> >
> >Any one can help me?
> >
> >Alberto
> >_______________________________________________
> >Insight-users mailing list
> >Insight-users@public.kitware.com
> >http://public.kitware.com/mailman/listinfo/insight-users
> 
> 
> -- 
> ===============================================
> Dr. Stephen R. Aylward
> Assistant Professor of Radiology
> Adjunct Assistant Professor of Computer Science
> http://caddlab.rad.unc.edu
> aylward@unc.edu
> (919) 966-9695
> 
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