Hi Cyrus, this may or may not be a problem. The cortical label in aseg.mgz is not used for this reason. Usually, the surface-based method will exclude the dura in these situations. Are the surfaces accurate or are they including dura as well? BTW, you should not be editing the aparc+aseg.mgz. doug
On 08/13/2012 01:04 PM, Sarosh, Cyrus wrote:
Hello FreeSurfer Users,
I looked for a possible solution to my problem in the Mail Archive and found this article referring to almost the exact same problem I am having:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314.html. Basically,pieces of the subarachnoid space/pia mater/arachnoid/dura mater/skull
are being segmented as the cortex in certain slices and this occurs when it is physically adjacent to the gray matter. Besides this point everything else seems to be running smooth.
In the related article I found that this may be caused by the MR parameters so I will give you the acquisition information that I know.
Theacquisitions are SPGRs, taken on either a GE 3T or 1.5T and the resolution is 1mm isotropic. Any solutions besides going through each series slice by
slice and making corrections would be greatly appreciated.
Thanks,
Cyrus
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