Hi Matthew,
In the script ${FSLDIR}/bin/siena_flow2std contains the line
${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow -dil -dil -dil -dil -dil -dil
-dil -dil -dil -dil -dil -dil -dil -dil ${A}_to_${B}_flow_dil
The help of avwmaths says
-dil : use (current image>0) to dilate using 3x3x3 neighourhood (new
value is average of non-zero neighbours)
That is a 26-connected greyscale dilation (in mathematical morphology
terms).
The calls to flirt in the siena_flirt script contain no parameters for
the interpolation, that means that the default is used. The help of
flirt says:
-interp {trilinear,nearestneighbour,sinc}
(final interpolation: def - trilinear)
HTH
Alle Meije
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?
>
>
>
> 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]
>
>
>
> 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.
>
>
>
> 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.
>
>
>
> Many thanks,
>
>
>
> Matthew Kempton
>
> Institute of Psychiatry
>
> London
>
>
>
>
>
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