Dear Freesurfer community,
1. Does the cortical segmentation (tinted red in the attached aseg_vs_pial.png) need to follow the pial surface (red line) precisely? Does the region under the cursor that is marked as cortex but is outside the pial surface count in the aparc results? In general, should I fix pial surfaces so that aseg and pial match precisely? For this participant, the skull strip and white matter segmentation both looked really good, especially in this region.
2. What about small pieces of remaining dura (or other outside brain material) labeled red as cortex in the aseg? Do they count in cortical thickness values, even though there's a clear gap between them and the cortex proper? (see cortex_outside_brain.png)
I did find this old post on the mailing list but I was unsure if it answers my question: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg03807.html
From what I gather from this post and some others*, the aparc results are
based on the surface and the aseg values are only relevant to subcortical structures, but I am still unsure if this is the correct interpretation. The original question in the mailing list concerns the hippocampus, but my questions are about the top of the cortex.
Many thanks for answers!
Ezra
* e.g., http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg07810.html *___________________________________________________________* *Ezra Wegbreit, PhD* NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Warren Alpert Medical School (401) 432-1615 ezra_wegbreit@brown.edu
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