All,
Upon looking at online forums and the FreeSurfer wiki, I have come to the understanding that "BrainSeg" volume in the aseg.stats file includes all cortical and subcortical gray matter, cerebellar gray matter; cortical, subcortical and cerebellar white matter and white matter hypointensities; and all ventricle volumes, but excludes the brain stem.
When using the aseg.stats file for included subject "bert" to check my understanding of which volumes are used, I cannot seem to produce identical "BrainSegVol-to-TIV" ratios.
I am adding the following volumes, all in mm^3, to obtain the brain volume:
TotalGrayVol: 658087.056198
CorticalWhiteMatterVol: 485627.161537
Left-Lateral-Ventricle: 6562.6
Left-Inf-Lat-Vent: 228.3
Left-Cerebellum-White-Matter: 15708.2
3rd-Ventricle: 997.5
4th Ventricle: 1714.2
Right-Lateral-Ventricle: 6039.9
Right-Inf-Lat-Vent: 160.3
Right-Cerebellum-White-Matter: 15694.5
5th-Ventricle: 14.1
WM-hypointensities: 1002.6
Sum of individual measures: 1191836.418
Output of BrainSegVol: 1193318
And when normalizing the subject's brain volume by the eTIV measure (1594882.911364), I obtain the following:
Individual measures: 0.7473
BrainSegVol-to-eTIV: 0.7482
Is there a reason that these two measurements are slightly off? I'm wondering whether there's certain volumes used for BrainSegVol that I missed, or ones that I included that would not be present in the output. Moreover, I'm wondering whether this could potentially be a result of using surface volumes (BrainSegVol) versus using both surface and voxel-space calculations (my addition method).
Any help is appreciated. Thank you in advance.
Best,
[1455168447449_PastedImage] Bernard L. Cook Biomedical Engineering | Class of 2017 BMES at Ohio State | Professional Development Chair '16-'17 IBRC | Undergraduate Research Assistant
440-623-4710 cook.1327@osu.edumailto:cook.1327@osu.edu
There are several ROIs you could be missing such as choroid plexus, vessel. Also, the BrainSegVol does not include partial volume correction which the aseg volumes will include, so you might be slightly off.
On 06/23/2016 12:47 PM, Cook, Bernie wrote:
All,
Upon looking at online forums and the FreeSurfer wiki, I have come to the understanding that "BrainSeg" volume in the aseg.stats file includes all cortical and subcortical gray matter, cerebellar gray matter; cortical, subcortical and cerebellar white matter and white matter hypointensities; and all ventricle volumes, but excludes the brain stem.
When using the aseg.stats file for included subject "bert" to check my understanding of which volumes are used, I cannot seem to produce identical "BrainSegVol-to-TIV" ratios.
I am adding the following volumes, all in mm^3, to obtain the brain volume:
TotalGrayVol: 658087.056198
CorticalWhiteMatterVol: 485627.161537
Left-Lateral-Ventricle: 6562.6
Left-Inf-Lat-Vent: 228.3
Left-Cerebellum-White-Matter: 15708.2
3rd-Ventricle: 997.5
4th Ventricle: 1714.2
Right-Lateral-Ventricle: 6039.9
Right-Inf-Lat-Vent: 160.3
Right-Cerebellum-White-Matter: 15694.5
5th-Ventricle: 14.1
WM-hypointensities: 1002.6
Sum of individual measures: 1191836.418
Output of BrainSegVol: 1193318
And when normalizing the subject's brain volume by the eTIV measure (1594882.911364), I obtain the following:
Individual measures: 0.7473
BrainSegVol-to-eTIV: 0.7482
Is there a reason that these two measurements are slightly off? I'm wondering whether there's certain volumes used for BrainSegVol that I missed, or ones that I included that would not be present in the output. Moreover, I'm wondering whether this could potentially be a result of using surface volumes (BrainSegVol) versus using both surface and voxel-space calculations (my addition method).
Any help is appreciated. Thank you in advance.
Best,
*1455168447449_PastedImage* Bernard L. Cook Biomedical Engineering | Class of 2017 BMES at Ohio State | Professional Development Chair '16-'17 IBRC| Undergraduate Research Assistant
440-623-4710 cook.1327@osu.edu mailto:cook.1327@osu.edu
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