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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: | Estimation of the gray matter and white matter volumes should be taken from the surfaces, and not from the aseg. If 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. Surface-based measures of cortical gray matter and white matter volume can be found in the header of the aseg.stats file: <<BR>>'''lhCortex''' & '''rhCortex''' - per hemi gray matter volume based on the pial surface <<BR>>'''Cortex''' - total gray matter volume based on the pial surface <<BR>>'''lhCorticalWhiteMatter''' & '''rhCorticalWhiteMatter''' - per hemi white matter volume based on the white surface <<BR>>'''!CorticalWhiteMatter''' - total white matter volume based on the white surface Here is how the above are calculated: |
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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. |
== 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>> == Other Volumes == In the aseg.stats header, you will also find the following volumes: <<BR>>'''!SubCortGray''' - volume-based measure of subcortical gray matter <<BR>>'''!TotalGray''' - '''Cortex''' + '''!SubCortGray''' <<BR>>'''!SupraTentorial''' - '''Cortex''' + '''!CorticalWhiteMatter''' + '''!SubCortGray''' (essentially, everything above the tentorium within the pial surface plus the subcortical volumes) '''!IntraCranialVol''' - estimated Total Intracranial vol (eTIV) ##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 should be taken from the surfaces, and not from the aseg. If 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.
Surface-based measures of cortical gray matter and white matter volume can be found in the header of the aseg.stats file:
lhCortex & rhCortex - per hemi gray matter volume based on the pial surface
Cortex - total gray matter volume based on the pial surface
lhCorticalWhiteMatter & rhCorticalWhiteMatter - per hemi white matter volume based on the white surface
CorticalWhiteMatter - total white matter volume based on the white surface
Here is how the above are calculated:
Volume = Surface Area x Thickness
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
Other Volumes
In the aseg.stats header, you will also find the following volumes:
SubCortGray - volume-based measure of subcortical gray matter
TotalGray - Cortex + SubCortGray
SupraTentorial - Cortex + CorticalWhiteMatter + SubCortGray (essentially, everything above the tentorium within the pial surface plus the subcortical volumes) IntraCranialVol - estimated Total Intracranial vol (eTIV)