What I normally do when I need a ROI from the atals:
a) fslview, open template, e.g. the mni152_brain_2mm
b) open the 'Atlas' tool, pick the Region of Interest, adding to the stack of images clicking on the '+' (bottom right corner of the regions' list window)
c) close the regions' list window
d) click on the region's 'layer', to make sure it is selected
e) File, save as, give a meaningful (and without spaces!) name -> fslview saves a nii.gz file containing your ROI, _in the same space of the anatomy it was displayed onto_.
f) Regardless of the visualization threshold you set in Fslview, the ROI is saved with its full range. -> you have to threshold at your taste.
For instance, a 50% left caudate binary mask would be obtained by:
fslmaths Left_caudate_saved_by_you -thr 50 -bin Left_caudate_thr50_mask
Hope this can help.
Kind regards,
Luca
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