Ezra,
The labeling of gm and wm that you see in the aseg.mgz file is not used to produce the cortical statistics found in the .stats files. The aseg.mgz grey matter appears this way because the aseg.mgz file is produced prior to running our 'surface stream', which produces the accurate gm/wm surface boundaries.
In our next release, v6.0 (which likely won't happen until January), we will have a 'cleaned-up' aseg.mgz, where gm and wm voxels are properly labeled with respect to the surfaces, to eliminate this confusion. Note that this is just a visualization improvement, not a change in accuracy of results found in aparc.stats.
In the meantime, if you would like to see what this 'cleaned-up' aseg looks like, then run the attached script from Doug Greve, like this:
cd <subjid>/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz
(you might want to rename the existing aseg.mgz if you want to compare new to old)
Nick
On Thu, 2014-10-16 at 14:08 -0400, Wegbreit, Ezra wrote:
Dear Freesurfer community,
- 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.
- 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
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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