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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 }}} 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 |
Volume = Surface Area x Thickness |
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| To get the white matter volume the program {{{mris_wm_volume}}} will calculate the wm volume, using the command: {{{ mris_wm_volume <subject> <hemi> }}} |
== 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: |
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| 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: <<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)