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Please refer to this site/make edits here for the most updated information: https://partnershealthcare.sharepoint.com/sites/LCN/SitePages/Morpho-Optimization-Project.aspx
Morphometry Stats and Global Measure of Volume
Note: on April 2, 2019, an error was found in the computation of some of these statistics with hires data analyzed in version 6. See this page for information about what is affected and how to fix it.
This page describes the various global measures of brain volume provided with FreeSurfer as of version 5.2 and later. 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 of 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 lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 235960.335754, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 234141.666979, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral 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.
lhCerebralWhiteMatter,rhCerebralWhiteMatter,CerebralWhiteMatter - volume inside the white surface minus anything that is not WM. CerebralWhiteMatter includes hypointensities. Does not include cerebellar white matter or brainstem. 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, putamen, pallidum, 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 and cerebellum with 5.2.
TotalGray - total gray matter volume. This is simply the sum of lhCortex + rhCortex + SubCortGray + 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);