[Insight-users] Creating 3D image object from a stack

[Stephen R. Aylward]

Sure.

We are working on a general solution to this problem, but in the 
meantime you can use the MetaImage reader - you just need to create a 
properly formated text file that describes how your data is stored - we 
call such text files "MetaImage" files.

The MetaImage format supports specifying a volume as a stack of 2D files 
or as a single file.   In the InsightApplications directory you can use 
MetaImageImporter to specify the text file that is parsed by the 
MetaImage reader to compose the volume.   Or you can easily specify that 
text file yourself.   The documentation for the MetaImage format is in 
Insight/Utilities/MetaIO/doc.

Basically, the text file should look like the following

NDims = 3
DimSize = 256 256 100
ElementSpacing = 1.0 1.0 1.0
BinaryDataByteOrderMSB = true   (or false if data is from a PC)
ElementType = MET_SHORT   (or MET_USHORT, MET_UCHAR, ....)
ElementDataFileName = LIST
<FilenameOfSlice0>
<FilenameOfSlice1>
...

or you can use printf style wildcards for the filenames by changing the 
ElementDataFileName tag such as

ElementDataFileName = filename%03d.raw 1 201 2

to specify the slices being in files called
filename001.raw
filename003.raw
filename005.raw
...
filename201.raw

I hope this helps.

Stephen

Gary O Tedeschi wrote:
> Hi,
> 
> Is there a way to read in a set of files, each holding a slice of a stack,
> so as to create a 3D itk::Image object?
> 
> thanks,
> Gary
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-- 
===============================================
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