Hi,

I think you'll need to threshold (fslmaths) the map using the structure number from the JHU-Labels.xml file in the atlas directory.

The relevant files are:

$FSLDIR/data/atlases/JHU-Labels.xml
$FSLDIR/data/atlases/JHU/JHU-WhiteMatter-labels-1mm.nii.gz

On 14 Sep 2009, at 16:18, Mithra wrote:

Hello FSL Users,

I have a question about using the While matter labels atlas

I would like to create  a mask of some White matter Structures under this atlas. For example - Middle Cerebral peduncle.
The problem with this atlas is its not probabilistic. I cannot point to this area and save this area like I can do with other atlases (like we can use the Subcortical structure atlas).
Is there a way to create masks using this White Matter Labels atlas?

Thank you for your help.

Regards,
Mithra.



-- 
Dave Flitney, IT Manager
Oxford Centre for Functional MRI of the Brain
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