[Insight-users] Bug in DICOM reader for 4D data?

[frankmiller at jhmi.edu]

Matthias,

I to am working with 4D MRI data and prefer to have it as a single 4D
volume. The method suggested in the 2004-May post doest work because the
ImageSeriesReader has no information about the fourth dimension. It sees
one big stack of 2D images.

My approach to this is to organize the images in my file system
as a series of directories grouped by time index. i.e. all slices from
time index 0 in directory 000/, all slices from time index 1 in
directory 001/, and so on. I then load the slices from each directory
into a 3D volume in the usual way with itk::ImageSeriesReader and use
the itk::TileImageFilter to group the 3D volume together into a 4D
volume. 

This solution seems less then ideal but it works.  Let me know if you
have any questions.

Frank

On Tue, Feb 06, 2007 at 12:18:27AM -0700, Matthias Schabel wrote:
> As per Luis' suggestion in a previous (fairly old) post (here :  
> http://public.kitware.com/pipermail/insight-users/2004-May/008568.html),
> I am attempting to get ITK to correctly read a 4D (time+volumetric)  
> dynamic MRI data set. With filenames ordered following the suggested
> grouping (chunked first by acquisition time, then by slice), when I  
> attempt to read, I end up with a 1 x 1620 x 192 x 176 volume. While
> the total number of voxels is correct, this should in fact be a 90 x  
> 18 x 192 x 176 volume. I have already verified independently that
> the time stamps are identical for all slices for each acquisition, so  
> this seems to me to be a bug in the DICOM reader. I really would prefer
> to have the data in the form of a single 4D volume rather than a  
> vector of 3D slices - any suggestions/workarounds?
> 
> Thanks,
> 
> Matthias
> 
> 
> ----------------------------------------------------------------
> Matthias Schabel, Ph.D.
> Assistant Professor, Department of Radiology
> Utah Center for Advanced Imaging Research
> 729 Arapeen Drive
> Salt Lake City, UT  84108
> 801-587-9413 (work)
> 801-585-3592 (fax)
> 801-706-5760 (cell)
> 801-484-0811 (home)
> mschabel at ucair dot med dot utah dot edu
> ----------------------------------------------------------------
> 
> 
> 
> 
> 
> 
> 
> 

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