Hi,
You could use "cluster" to create a map of cluster index and
then remove all but the largest clusters. This would be
better than morphological operations (erode, dilate, etc)
as it will not change the boundaries of the large rois.
The command you want is
cluster -i maskimage -t 1 --osize=newmaskimage
Then you re-threshold newmaskimage based on the size of
the smallest acceptable cluster
e.g. fslmaths newmaskimage -thr 3 -bin newmaskimage
All the best,
Mark
On 19 Nov 2007, at 23:50, Dianne Patterson wrote:
> Dear group,
> I am trying to identify hyperintensities on a flair image.
> By brain stripping and eroding the edge of the flair, I get an image
> which is pretty suitable for thresholding.
> However, I get quite a few little single voxels (or VERY small areas)
> passing the threshold.
> Is there some way in FSL to clean up my thresholded binary image to
> remove these very tiny rois?
>
> Thankyou,
>
> Dianne
>
>
> --
> Dianne Patterson, Ph.D.
> [log in to unmask]
> ERP Lab
> University of Arizona
> 621-3256 (Office)
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