Hi Roman,

You can get the subcortical names from:
   http://www.fmrib.ox.ac.uk/fsl/first/cma_subcortical_label.html
and the cortical names from:
  $FSLDIR/data/atlases/HarvardOxford-Cortical.xml
(although for the latter you need to add one to the index number to 
 get the equivalent number in the nifti image).

So a simple script call should be able to extract the name for you.

All the best,
Mark


On 26 Oct 2011, at 22:22, Roman M wrote:

Hi, is there a straightforward way of parceling the atlases (e.g., the Harv-Oxford cortical/subcortical) in individual files, one per homogeneous region, each with the correct name? I can see using fslmaths -thr and -uthr to threshold the image at each value, but how would I then get the mask name (if not manually)?

 thank you

 Roman