Hi Jongho - if you run the fsl program "avwhd" on the analyze file you
should see in there something like
dim0 4
dim1 64
dim2 128
dim3 1
dim4 240
where dim0 is the dimensionality (often ignored),
dim1 and 2 are x and y dimensions of the axial slices
dim3 is the number of slices in a volume (which is 1 if you have single
slice data, even if it is multiple time points)
dim4 is the number of time points.
If your matlab analyze writing script is correct, this should all appear
fine. Does this answer your question?
For running BET - note that BET is really designed for full 3D datasets.
There is a cheap kludge in BET to _try_ to work on single slice data, but
it's not very tested and may not work well. Do you really need to do brain
extraction on the 2D images?
Thanks, Steve.
On Wed, 20 Aug 2003, Jongho Lee wrote:
> Hello --
> I tried to put only two anatomical images (axial images with matlab data
> sets) in 4-D format(.img and .hdr files to process BET) in various ways
> but I cannot view it properly with 'slices'. How should I put them in 4-D
> format? What should be the values of T or z? What about I have two slices
> of axial images and two slices of sagittal images? Do I need to have all 3
> axises? I'm mostly using matlab to process byproducts of scanner and FSL.
> Please help me. Thank you.
>
> Jongho Lee
>
Stephen M. Smith MA DPhil CEng MIEE
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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