Hi Matthew,
Thank you for your response! 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?
Thank you!
Cristina
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