This is a bug in fslview - as a workaround you can generate the mask you want by using fslmaths and the -thr -uthr options on the atlas image file to select the label you want a mask of.
> Hello FSL Experts,
> I have been encountering an issue while trying to create white matter masks using the JHU ICBM-DTI-81 White Matter Atlas. When choosing the genu of the corpus callosum, for example, the tract that shows up is incorrect (see attached). Any ideas of why this may be happening or how to fix it?
> Below are the steps I am following to create anatomical masks.
> 1. Open FSLview
> 2. Open a standard brain
> 3. Click on "Atlas Tools" from the "Tools" drop down menu
> 4. Click on "Atlases" and select the JHU ICBM-81 White Matter Labels atlas or Tractography Atlas
> 5. Click on "Structures," choose "JHU ICBM-DTI-81 White Matter Labels" from the drop down
> 6. Select my structure (e.g., genu of corpus callosum), click the plus sign [this is when the incorrect tract (example attached to my last post) shows up]
> 7. Save image using "Save as"
> 8. Threshold (~10) and binarize my newly saved image
> The entire process works well when I use the Tractography Atlas (i.e., appears to display correct tracts), but when I try to choose a tract from the JHU ICBM 81 atlas, the picture I sent shows up. Any ideas of what might be going on?
> Any help with this would be much appreciated!!!
> Thank you,
> <Screen Shot 2014-08-25 at 9.55.34 PM.png>