Hi Jen,
1) open fslview and then open via <File/Open standard ... > one of
the standard brains.
2) go to Tools/Toolbars/Atlastools
3) in the atlastoolbar hit the Structures button and select the atlas
and structure (e.g. hippocampus) that you're interested in (make sure
that you selected Preview selected structure probability map)
4) Save the overlay via File/Save under any name you like (e.g.
hippocampus_mask)
5) use fslmaths to change the mask according to your needs e.g.
fslmaths hippocampus_mask -thr 50 hippocampus_mask_thr50 will give you
a new mask with only voxels that have a probability of over 50
belonging to that structure, you can also binarise this mask with
fslmaths hippocampus_mask_thr50 -bin ippocampus_mask_thr50_binarized
(just enter fslmaths to see what options you have with fslmaths -
there are quite a bit)
Does that help?
cheers, michael
On 16-Mar-09, at 2:07 PM, Jennifer Bramen wrote:
> Dear FSL List
>
> I would like to use individual regions of interest from one of the
> free atlases. However, the
> atlases are composed of multiple regions and I do not know how to
> create a separate mask
> for an individual region. Is there a command I can use?
>
> Thanks
>
> jen
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