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= Morphometry Stats and Global Measure of Volume (5.2 and 5.3) =

This page describes the various global measures of brain volume provided with FreeSurfer as of version 5.2 and 5.3. To see the same for version 6, goto MorphometryStats. The calculations
are not as simple as just adding up the number of voxels in a particular structure because we exploit the fact that we can get much better accuracy with surface-based calculations. For 5.2 and later, brain stem is not included in these measures because the amount of brain stem changes depending upon the field of view of the volume acquisition.

After recon-all finishes, there will be a file called subject/stats/aseg.stats. This is a table volume and intensity
statistics for each segmentation. It also contains the following metrics:


{{{
# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1126237.000000, mm^3
# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1111880.000000, mm^3
# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 241564.568351, mm^3
# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 233961.051724, mm^3
# Measure Cortex, CortexVol, Total cortical gray matter volume, 475525.620074, mm^3
# Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 235960.335754, mm^3
# Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 234141.666979, mm^3
# Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 470102.002733, mm^3
# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 55372.000000, mm^3
# Measure TotalGray, TotalGrayVol, Total gray matter volume, 611801.620074, mm^3
# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1016590.622807, mm^3
# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1002233.622807, mm^3
# Measure Mask, MaskVol, Mask Volume, 1556214.000000, mm^3
# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1480005.051398, mm^3
}}}


'''!BrainSeg''' - volume of all voxels in the aparc+aseg.mgz that are neither
background nor brain stem. This is the same as pre-5.2 versions except
that brain stem is not included. This will also include the "vessel",
"optic-chiasm", and "CSF" segmentations. This is just a simple count
of voxels in aparc+aseg.mgz. There are also additional stats for voxel-based supratentorial volume and surface based brain seg volume.

'''!BrainSegNotVent''' - same as !BrainSeg without ventricles (lateral,
inferior lateral, 3rd, 4th, 5th), CSF, and choroid plexus.

'''lhCortex,rhCortex,Cortex''' - volume inside the pial surface minus the volume
inside the white surface minus tissue inside the ribbon that is not
part of cortex (eg, hippocampus). This uses the surface-based volume
calculation and is not a voxel count. It is approximately equal to the
count of cortical label voxels in aparc+aseg.mgz.

'''lhCorticalWhiteMatter,rhCorticalWhiteMatter,!CorticalWhiteMatter'''
- volume inside the white surface minus anything that is not
WM. !CorticalWhiteMatter includes hypointensities. This uses the
surface-based volume computation for part of the calculation and
counts voxels to subtract "anything not in WM". It is approximately equal
to the count of WM voxels in aparc+aseg.mgz.

'''!SubCortGray''' - includes thalamus, caudate, hippocampus, amygdala,
accumbens, ventral DC, substancia nigra (if there). This is a simple
voxel count of structures identified as subcortical GM. The function
used to define this is !IsSubCorticalGray() in cma.c. NOTE:
!SubCortGray excludes brain stem with 5.2.

'''!TotalGray''' - total gray matter volume. This is simply the sum of
!SubCortGray + lhCortex + rhCortex + CerebellumGM. As such, it includes
both surface-based volume calculations and voxel counts.

'''!SupraTentorial''' - includes everything except cerebellum (GM and WM) and
brain stem. It is computed based on everything inside the pial surface
plus any structures that might fall partially or totally outside of the pial, e.g.,
hippocampus, amygdala, corpus callosum, ventral DC, thalamus,
ventricles, and choroid plexus. The function that determines the
volume of structures outside of the supratentorium is
!SupraTentorialVolCorrection() in cma.c. Note that !SupraTentorial
includes ventricle, choroid plexus, and vessel. This uses
surface-based volume calculations and voxel counts.

'''!SupraTentorialNotVent''' - same as SupraTentorial but subracting
the volume ventricles (lateral,inferior lateral, 3rd, 4th, 5th), CSF, and choroid plexus.

'''Mask''' - count of non-zero voxels in the brainmask.mgz. In general, this
is not useful for reporting results but might be handy for QA.

'''!EstimatedTotalIntraCranialVol''' (eTIV) - This is the same number as the
!IntraCrainialVol (ICV) from pre-5.2 verions. The name was changed to
help avoid confusion as to what this number is and is not. It is NOT is a
count of voxels inside the skull. The eTIV is a metric computed from the
amount of scaling in the talairach.xfm file.
See http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV.


The above metrics are computed using the following function in cma.c:
{{{
BrainVolStats = (double *)ComputeBrainVolumeStats(subject);
}}}

##The program mris_volume will compute the volume inside a surface. It should be run from within the <subjid>/surf directory with the following command:
##{{{
##mris_volume ?h.surface
##}}}
##where {{{?h.surface}}} is replaced with the specific surface you are looking for the volume of.

##To get the gray matter volume you should use the following formula:
##{{{
##gm volume = pial volume - white volume
##}}}

##To get the white matter volume the program {{{mris_wm_volume}}} will calculate the wm volume, using the command:
##{{{
##mris_wm_volume <subject> <hemi>
##}}}