Re: [Freesurfer] BrainSeg Volume Clarification

2016-07-07 Thread Douglas N Greve 
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.1...@osu.edu 
>
>
>
>
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-- 
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[Freesurfer] BrainSeg Volume Clarification

2016-06-23 Thread Cook, Bernie 
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.1...@osu.edu


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.