Hi Alyssa,

the orbital stuff might be fat that has shifted into brain, for which there's really nothing that can be done except fix the acquisition (change the read-out direction or increase the bandwidth or both). Not sure what's up with the other spot. Is the nearby white matter intensity significantly less than 110? If so, some control points in the wm might help. If not you would need to upload the dataset so we can take a look Bruce

On Sat, 3 Aug 2013, Zhu, Alyssa wrote:

Hi,

Is there a way to get the various intensity abnormality labels (100-117) seen in the FreeSurferColorLUT.txt file (e.g. via a different command line option)? Thus far we've only been getting the WM-hypointensities (77) and non-WM-hypointensities (80) labels. I read in another thread that some labels are no longer used in current versions (my lab is using v5.1). Is that the case here?

Thanks, Alyssa