Hi,
On 1 Aug 2007, at 16:58, Kempton, Matthew wrote:
> Dear FSLs
>
> After submitting a paper which uses a SIENA voxelwise analysis I
> have been asked the following questions by a reviewer:
>
> 1) For the dilation used in SIENA what is the structural
> element used with this operator?
In FSL3.3 it is 14x a 3x3x3 kernel non-binary dilation, but the exact
details don't make any difference as long as the dilation is larger
than the required shift between the actual edges and the native-space-
transformed version of the standard space edges.
> 2) What type of interpolation (nearest neighbour, splines
> etc.) is used when the aligned images are transformed to space
> halfway between them [this is done in the first part of siena_diff]
Trlinear.
> For 1) I have looked at the script siena_flow2std and can see
> avwmaths is used and the ‘-dil’ command is used 14 times but I’m
> still not sure what the structural element is.
The avwmaths command line usage tells you this ;-)
> For 2) I have tried to find the answer in the siena_flirt script
> but I am still not sure what type of interpolation is used.
Indeed - it's not explicitly set in the flirt calls which means that
the default is used - trlinear.
Cheers.
>
>
> Many thanks,
>
>
>
> Matthew Kempton
>
> Institute of Psychiatry
>
> London
>
>
>
>
>
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR 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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