Hi all, I want to pull the measure of whole brain volume. In the aseg.stats there is a BrainMaskVol and a BrainSegVol. Which one do I want? As I understand it, BrainMaskVol is the volume of the brainmask (including the ventricles) whereas BrainSegVol is the volume of brain matter and not including the ventricles, so I think this is the one I want, but I want to make sure and I couldn't find a straight answer on the wiki. Thanks! Akram.
This is from mri_segstats --help
MEASURES OF BRAIN VOLUME
There will be four measures of brain volume in the output summary file: (1) BrainSegNotVent - sum of the volume of the structures identified in the aseg.mgz volume this will include cerebellum but not ventricles, CSF and dura. Includes partial volume compensation with --pv. This is probably the number you want to report. (2) BrainMask - total volume of non-zero voxels in brainmask.mgz. This will include cerebellum, ventricles, and possibly dura. This is probably not what you want to report. (3) BrainSeg - sum of the volume of the structures identified in the aseg.mgz volume. This will include cerebellum and ventricles but should exclude dura. This does not include partial volume compensation, so this number might be different than the sum of the segmentation volumes. (4) IntraCranialVol (ICV) - estimate of the intracranial volume based on the talairach transform. See surfer.nmr.mgh.harvard.edu/fswiki/eTIV for more details. This is the same measure as Estimated Total Intracranial Volume (eTIV).
Akram Bakkour wrote:
Hi all, I want to pull the measure of whole brain volume. In the aseg.stats there is a BrainMaskVol and a BrainSegVol. Which one do I want? As I understand it, BrainMaskVol is the volume of the brainmask (including the ventricles) whereas BrainSegVol is the volume of brain matter and not including the ventricles, so I think this is the one I want, but I want to make sure and I couldn't find a straight answer on the wiki. Thanks! Akram.
this wiki page has just been created to hold this info:
http://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume
On Wed, 2007-11-28 at 14:14 -0500, Doug Greve wrote:
This is from mri_segstats --help
MEASURES OF BRAIN VOLUME
There will be four measures of brain volume in the output summary file: (1) BrainSegNotVent - sum of the volume of the structures identified in the aseg.mgz volume this will include cerebellum but not ventricles, CSF and dura. Includes partial volume compensation with --pv. This is probably the number you want to report. (2) BrainMask - total volume of non-zero voxels in brainmask.mgz. This will include cerebellum, ventricles, and possibly dura. This is probably not what you want to report. (3) BrainSeg - sum of the volume of the structures identified in the aseg.mgz volume. This will include cerebellum and ventricles but should exclude dura. This does not include partial volume compensation, so this number might be different than the sum of the segmentation volumes. (4) IntraCranialVol (ICV) - estimate of the intracranial volume based on the talairach transform. See surfer.nmr.mgh.harvard.edu/fswiki/eTIV for more details. This is the same measure as Estimated Total Intracranial Volume (eTIV).
Akram Bakkour wrote:
Hi all, I want to pull the measure of whole brain volume. In the aseg.stats there is a BrainMaskVol and a BrainSegVol. Which one do I want? As I understand it, BrainMaskVol is the volume of the brainmask (including the ventricles) whereas BrainSegVol is the volume of brain matter and not including the ventricles, so I think this is the one I want, but I want to make sure and I couldn't find a straight answer on the wiki. Thanks! Akram.
Great! Thanks! My subjects were ran in stable3, so they didn't have the BrainSegVolNotVent measure in the aseg.stats. Rerunning segstats though.. Thanks again!
On Wed, 28 Nov 2007, Nick Schmansky wrote:
this wiki page has just been created to hold this info:
http://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume
On Wed, 2007-11-28 at 14:14 -0500, Doug Greve wrote:
This is from mri_segstats --help
MEASURES OF BRAIN VOLUME
There will be four measures of brain volume in the output summary file: (1) BrainSegNotVent - sum of the volume of the structures identified in the aseg.mgz volume this will include cerebellum but not ventricles, CSF and dura. Includes partial volume compensation with --pv. This is probably the number you want to report. (2) BrainMask - total volume of non-zero voxels in brainmask.mgz. This will include cerebellum, ventricles, and possibly dura. This is probably not what you want to report. (3) BrainSeg - sum of the volume of the structures identified in the aseg.mgz volume. This will include cerebellum and ventricles but should exclude dura. This does not include partial volume compensation, so this number might be different than the sum of the segmentation volumes. (4) IntraCranialVol (ICV) - estimate of the intracranial volume based on the talairach transform. See surfer.nmr.mgh.harvard.edu/fswiki/eTIV for more details. This is the same measure as Estimated Total Intracranial Volume (eTIV).
Akram Bakkour wrote:
Hi all, I want to pull the measure of whole brain volume. In the aseg.stats there is a BrainMaskVol and a BrainSegVol. Which one do I want? As I understand it, BrainMaskVol is the volume of the brainmask (including the ventricles) whereas BrainSegVol is the volume of brain matter and not including the ventricles, so I think this is the one I want, but I want to make sure and I couldn't find a straight answer on the wiki. Thanks! Akram.
freesurfer@nmr.mgh.harvard.edu
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Akram Bakkour -
Doug Greve -
Nick Schmansky