[Insight-users] MR volume: slice location + spacing pb

[Stephen R. Aylward]

MR can be acquired with spacing difference from slice thickness, and 
with either varying throughout the volume.

If the spacing/thickness is constant throughtout the volume: All that 
you can hope to do is assume that slice spacing is the same as slice 
thickness - I have no idea how to program a gradient filter that handles 
differences in spacing and thickness. My suggestion is to ignore 
thickness and use only spacing.

If the MR was acquired with difference spacing/thickness throughout the 
volume... the itk image format doesn't support such data - you must 
derive a class from the image class.   Also, most of the filters won't 
work correctly (generally they only check slice thickness once, and use 
it for all subsequent calculations - only perhaps some of the 
registration stuff done in physical coordinates will work).

There are some packages that deal with such data - PLUNC is one such 
package that can be licensed - it is intended for radiation therapy 
treatment planning - such funky MR/CT protocols are common in radonc.

Good luck,
Stephen

Dean Inglis wrote:
> Has anyone found a way to deal
> with MR aquisitions that report subsequent slice 
> locations that do not correspond to the reported
> DICOM header slice thickness?  That is, all DICOM
> headers in the series report an isotropic out of
> plane slice thickness yet the difference in slice 
> location can be different between slices.  I am 
> trying to do orthogonal MPR with this type of data.
> Any ideas/comments would be great.
> 
> thanks,
> Dean 
> 
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-- 
===========================================================
Dr. Stephen R. Aylward
Associate Professor of Radiology
Adjunct Associate Professor of Computer Science and Surgery
http://caddlab . rad . unc . edu
aylward at unc . edu
(919) 966-9695