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| Estimation of the gray matter and white matter volumes should be taken from the surfaces, and not from the aseg. 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: | == Gray Matter and White Matter Volume == Estimation of the gray matter and white matter volumes is calculated from the surfaces and not from the aseg labels. <<BR>>It is worth noting that in cases where the data is of very poor quality and surfaces cannot be reconstructed, but the aseg is fairly accurate, then gm and wm volume can be taken from the aseg (this will require an extra flag to get these values in the stats files instead of the surface-based values). Surface-based volume is calculated as: |
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| mris_volume ?h.surface | Volume = Surface Area x Thickness |
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| where {{{?h.surface}}} is replaced with the specific surface you are looking for the volume of. | |
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| To get the gray matter and white matter volumes you should use the following formulas: {{{ gm volume = pial volume - white volume wm volume = white volume - (ventricles+caudate+putamen+pallidum+thalamus)* }}} * the subcortical volumes can be taken from the aseg.stats file. |
Surface-based measures of cortical gray matter and white matter volume can be found in the header of the aseg.stats file. Below, the names of these measures are listed along with how they are defined: <<BR>>'''lhCortex''' & '''rhCortex''' -> per hemi gray matter volume based on the pial surface *everything between the pial and white surface for that hemisphere excluding any of the following that may fall within the pial surface (as labeled by the aseg.mgz): subcortical gray matter (full list below in Additional Calculated Volumes section), ventricles, vessels, and choroid plexus. <<BR>>'''Cortex''' -> total gray matter volume (lh + rh) based on the pial surface *everything between the pial and white surface for both hemispheres excluding any of the following that may fall within the pial surface (as labeled by the aseg.mgz): subcortical gray matter (full list below in Additional Calculated Volumes section), ventricles, vessels, and choroid plexus. <<BR>>'''lhCorticalWhiteMatter''' & '''rhCorticalWhiteMatter''' -> per hemi white matter volume based on the white surface *everything within the white surface for that hemisphere excluding any of the following that may fall within the white surface (as labeled by the aseg.mgz): subcortical gray matter (full list below in Additional Calculated Volumes section), ventricles, vessels, and choroid plexus. <<BR>>'''!CorticalWhiteMatter''' -> total white matter volume (lh + rh) based on the white surface *everything within the white surface for both hemispheres excluding any of the following that may fall within the white surface (as labeled by the aseg.mgz): subcortical gray matter (full list below in Additional Calculated Volumes section), ventricles, vessels, and choroid plexus. ##More specifically, the '''!CorticalWhiteMatter''' measurement is calculated by determining which voxels are within the WM surface. Only the voxels with the following labels in the aseg are counted: ##Left_Cerebral_Cortex, Right_Cerebral_Cortex, Left_Cerebral_White_Matter, Right_Cerebral_White_Matter, Left_WM_hypointensities, Right_WM_hypointensities, CC_Posterior, CC_Mid_Posterior, CC_Central, ##CC_Mid_Anterior, and CC_Anterior. ##'''Note''': The *_Cortex labels are included when calculating the '''!CorticalWhiteMatter''' measurement to catch the partially volumed voxels. == Additional Calculated Volumes == In the aseg.stats header, you will also find the following volumes: <<BR>>'''!SubCortGray''' -> volume-based measure of subcortical gray matter based on the labeled structures in the aseg.mgz *thalamus, caudate, putamen, pallidum, hippocampus, amygdala, accumbens, VentralDC, cerebellar cortex, brain stem (note: brain stem will not be included in version 5.2 and higher). <<BR>>'''!TotalGray''' -> '''Cortex''' + '''!SubCortGray''' *everything between the pial and white surface for both hemispheres + thalamus, caudate, putamen, pallidum, hippocampus, amygdala, accumbens, VentralDC <<BR>>'''!SupraTentorial''' -> '''Cortex''' + '''!CorticalWhiteMatter''' + '''!SubCortGray''' (essentially, everything above the tentorium within the pial surface plus the subcortical volumes) *everything within both the pial and white surfaces + lateral ventricles, inferior lateral ventricles, choroid plexus, wm hypointensities, corpus callosum, thalamus, caudate, putamen, pallidum, hippocampus, amygdala, accumbens, VentralDC. <<BR>>'''!IntraCranialVol''' -> estimated Total Intracranial vol ([[eTIV|eTIV]]) == Subcortical Volumes == The volume for all the subcortical structures segmented by the aseg.mgz can also be found in the aseg.stats file. For each structure, you will find the number of voxels, mean intensity across the structure, the standard deviation, Min, Max and Range of the intensity across the structure. The structures that are segmented are: Left-Lateral-Ventricle<<BR>> Left-Inf-Lat-Vent<<BR>> Left-Cerebellum-White-Matter<<BR>> Left-Cerebellum-Cortex<<BR>> Left-Thalamus-Proper<<BR>> Left-Caudate<<BR>> Left-Putamen<<BR>> Left-Pallidum<<BR>> 3rd-Ventricle<<BR>> 4th-Ventricle<<BR>> Brain-Stem<<BR>> Left-Hippocampus<<BR>> Left-Amygdala<<BR>> CSF<<BR>> Left-Accumbens-area<<BR>> Left-VentralDC<<BR>> Left-vessel<<BR>> Left-choroid-plexus<<BR>> Right-Lateral-Ventricle<<BR>> Right-Inf-Lat-Vent<<BR>> Right-Cerebellum-White-Matter<<BR>> Right-Cerebellum-Cortex<<BR>> Right-Thalamus-Proper<<BR>> Right-Caudate<<BR>> Right-Putamen<<BR>> Right-Pallidum<<BR>> Right-Hippocampus<<BR>> Right-Amygdala<<BR>> Right-Accumbens-area<<BR>> Right-VentralDC<<BR>> Right-vessel<<BR>> Right-choroid-plexus<<BR>> 5th-Ventricle<<BR>> WM-hypointensities<<BR>> Left-WM-hypointensities<<BR>> Right-WM-hypointensities<<BR>> non-WM-hypointensities<<BR>> Left-non-WM-hypointensities<<BR>> Right-non-WM-hypointensities<<BR>> Optic-Chiasm<<BR>> CC_Posterior<<BR>> CC_Mid_Posterior<<BR>> CC_Central<<BR>> CC_Mid_Anterior<<BR>> CC_Anterior<<BR>> ##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> ##}}} |
Morphometry Stats
Gray Matter and White Matter Volume
Estimation of the gray matter and white matter volumes is calculated from the surfaces and not from the aseg labels.
It is worth noting that in cases where the data is of very poor quality and surfaces cannot be reconstructed, but the aseg is fairly accurate, then gm and wm volume can be taken from the aseg (this will require an extra flag to get these values in the stats files instead of the surface-based values).
Surface-based volume is calculated as:
Volume = Surface Area x Thickness
Surface-based measures of cortical gray matter and white matter volume can be found in the header of the aseg.stats file. Below, the names of these measures are listed along with how they are defined:
lhCortex & rhCortex -> per hemi gray matter volume based on the pial surface
- everything between the pial and white surface for that hemisphere excluding any of the following that may fall within the pial surface (as labeled by the aseg.mgz): subcortical gray matter (full list below in Additional Calculated Volumes section), ventricles, vessels, and choroid plexus.
Cortex -> total gray matter volume (lh + rh) based on the pial surface
- everything between the pial and white surface for both hemispheres excluding any of the following that may fall within the pial surface (as labeled by the aseg.mgz): subcortical gray matter (full list below in Additional Calculated Volumes section), ventricles, vessels, and choroid plexus.
lhCorticalWhiteMatter & rhCorticalWhiteMatter -> per hemi white matter volume based on the white surface
- everything within the white surface for that hemisphere excluding any of the following that may fall within the white surface (as labeled by the aseg.mgz): subcortical gray matter (full list below in Additional Calculated Volumes section), ventricles, vessels, and choroid plexus.
CorticalWhiteMatter -> total white matter volume (lh + rh) based on the white surface
- everything within the white surface for both hemispheres excluding any of the following that may fall within the white surface (as labeled by the aseg.mgz): subcortical gray matter (full list below in Additional Calculated Volumes section), ventricles, vessels, and choroid plexus.
Additional Calculated Volumes
In the aseg.stats header, you will also find the following volumes:
SubCortGray -> volume-based measure of subcortical gray matter based on the labeled structures in the aseg.mgz
- thalamus, caudate, putamen, pallidum, hippocampus, amygdala, accumbens, VentralDC, cerebellar cortex, brain stem (note: brain stem will not be included in version 5.2 and higher).
TotalGray -> Cortex + SubCortGray
- everything between the pial and white surface for both hemispheres + thalamus, caudate, putamen, pallidum, hippocampus, amygdala, accumbens, VentralDC
SupraTentorial -> Cortex + CorticalWhiteMatter + SubCortGray (essentially, everything above the tentorium within the pial surface plus the subcortical volumes)
- everything within both the pial and white surfaces + lateral ventricles, inferior lateral ventricles, choroid plexus, wm hypointensities, corpus callosum, thalamus, caudate, putamen, pallidum, hippocampus, amygdala, accumbens, VentralDC.
IntraCranialVol -> estimated Total Intracranial vol (eTIV)
Subcortical Volumes
The volume for all the subcortical structures segmented by the aseg.mgz can also be found in the aseg.stats file. For each structure, you will find the number of voxels, mean intensity across the structure, the standard deviation, Min, Max and Range of the intensity across the structure. The structures that are segmented are:
Left-Lateral-Ventricle
Left-Inf-Lat-Vent
Left-Cerebellum-White-Matter
Left-Cerebellum-Cortex
Left-Thalamus-Proper
Left-Caudate
Left-Putamen
Left-Pallidum
3rd-Ventricle
4th-Ventricle
Brain-Stem
Left-Hippocampus
Left-Amygdala
CSF
Left-Accumbens-area
Left-VentralDC
Left-vessel
Left-choroid-plexus
Right-Lateral-Ventricle
Right-Inf-Lat-Vent
Right-Cerebellum-White-Matter
Right-Cerebellum-Cortex
Right-Thalamus-Proper
Right-Caudate
Right-Putamen
Right-Pallidum
Right-Hippocampus
Right-Amygdala
Right-Accumbens-area
Right-VentralDC
Right-vessel
Right-choroid-plexus
5th-Ventricle
WM-hypointensities
Left-WM-hypointensities
Right-WM-hypointensities
non-WM-hypointensities
Left-non-WM-hypointensities
Right-non-WM-hypointensities
Optic-Chiasm
CC_Posterior
CC_Mid_Posterior
CC_Central
CC_Mid_Anterior
CC_Anterior