Hi - like most analysis programs, FSL programs assume that any
between-slice spacing is already included in the "slice thickness"
dimension, not as a separate measurement. If you just view the image with
slices or fslview you should see whether the aspect ratio looks wrong. If
so, adjust the header with for example avwcreatehd.
Cheers.
On Fri, 13 Feb 2004, Lee, Sang wrote:
> Hello, everyone...
>
> Does FSL programs (etc. BET, FAST) recognize slice spacing on 3D volume
> sets?
> For example, one of our 3D axial images have 2.2mm slice thinkness and 1.1mm
> slice overlap, meaning each slice is only 1.1mm thick.
>
> When i run BET with this images, I get large volume of brain. (approximately
> 2X)
> I want to make sure if it is result of slice spacing.
> If slice spacing is the problem, is there a way for me to tell the program
> to count slice spacing?
>
> Thank you.
>
> Aaron Lee****************************EMAIL
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Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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