[Freesurfer] FreeSurfer High Resolution vs. Low Resolution Volume Discrepancy
External Email - Use Caution Dear FreeSurfer Community, In processing high-resolution (0.7 mm^3 isotropic) and low resolution (1.0 mm^3 isotropic) versions of the same data we have received conflicting volume data in our aseg.stats file. Below is the relevant excerpt from those files. High-resolution (0.7 mm^3 isotropic) # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 3264609.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 3192286.00, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1330806.023066, mm^3 # Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 60940.00, mm^3 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 230160.306401, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 228696.462181, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 458856.768582, mm^3 # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 158718.858711, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 161112.395773, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 319831.254484, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 149905.00, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 941078.768582, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 970862.023066, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 909922.023066, mm^3 # Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 2790169.00, mm^3 # Measure Mask, MaskVol, Mask Volume, 4652001.00, mm^3 # Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 2.065785, unitless # Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 2.943701, unitless # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 46, unitless # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 70, unitless # Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 116, unitless # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1580323.941985, mm^3 Low resolution (1.0 mm^3 isotropic) # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1132377.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1107596.00, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1106786.650039, mm^3 # Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 21069.00, mm^3 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 226998.297110, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 225122.819041, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 452121.116151, mm^3 # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 228780.783147, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 235221.750741, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 464002.533888, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 51537.00, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 619358.116151, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 990616.650039, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 969547.650039, mm^3 # Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 968494.00, mm^3 # Measure Mask, MaskVol, Mask Volume, 1574410.00, mm^3 # Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 0.714626, unitless # Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 0.993586, unitless # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 30, unitless # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 27, unitless # Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 57, unitless # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1584573.435767, mm^3 Some of the measures, like eTIV, lhCortexVol and rhCortexVol are in good agreemen
Re: [Freesurfer] FreeSurfer High Resolution vs. Low Resolution Volume Discrepancy
External Email - Use Caution Dear Gaurav Verma, this should fix your issue: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Verma, Gaurav Gesendet: Dienstag, 21. Mai 2019 17:34 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] FreeSurfer High Resolution vs. Low Resolution Volume Discrepancy External Email - Use Caution Dear FreeSurfer Community, In processing high-resolution (0.7 mm^3 isotropic) and low resolution (1.0 mm^3 isotropic) versions of the same data we have received conflicting volume data in our aseg.stats file. Below is the relevant excerpt from those files. High-resolution (0.7 mm^3 isotropic) # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 3264609.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 3192286.00, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1330806.023066, mm^3 # Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 60940.00, mm^3 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 230160.306401, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 228696.462181, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 458856.768582, mm^3 # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 158718.858711, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 161112.395773, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 319831.254484, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 149905.00, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 941078.768582, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 970862.023066, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 909922.023066, mm^3 # Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 2790169.00, mm^3 # Measure Mask, MaskVol, Mask Volume, 4652001.00, mm^3 # Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 2.065785, unitless # Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 2.943701, unitless # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 46, unitless # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 70, unitless # Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 116, unitless # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1580323.941985, mm^3 Low resolution (1.0 mm^3 isotropic) # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1132377.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1107596.00, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1106786.650039, mm^3 # Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 21069.00, mm^3 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 226998.297110, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 225122.819041, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 452121.116151, mm^3 # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 228780.783147, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 235221.750741, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 464002.533888, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 51537.00, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 619358.116151, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 990616.650039, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 969547.650039, mm^3 # Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 968494.00, mm^3 # Measure Mask, MaskVol, Mask Volume, 1574410.00, mm^3 # Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 0.714626, unitless # Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 0.993586, unitless # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 30, unitless # Measure
Re: [Freesurfer] FreeSurfer High Resolution vs. Low Resolution Volume Discrepancy {Disarmed}
External Email - Use Caution Thank you so much, Falk! That addresses my concerns perfectly! Gaurav From: falk.luesebr...@med.ovgu.de Sent: Wednesday, May 22, 2019 2:28:06 AM To: freesurfer@nmr.mgh.harvard.edu Cc: Verma, Gaurav Subject: AW: [Freesurfer] FreeSurfer High Resolution vs. Low Resolution Volume Discrepancy Dear Gaurav Verma, this should fix your issue: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed<https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_BrainVolStatsFixed&d=DwMFAw&c=shNJtf5dKgNcPZ6Yh64b-A&r=-xjBtbv9C0Nj0hNC2B8e4qtUhrAVR_Iqm_w7_DczG-k&m=Ku4pQ9rs8ggb18RQ_FnAN-Tk5GJGz8gY6f-E9_MEq3g&s=jsFV-A7_w7H3ZhlYig5pieCJJ3z3HMHUefS01PPo9A4&e=> Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Verma, Gaurav Gesendet: Dienstag, 21. Mai 2019 17:34 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] FreeSurfer High Resolution vs. Low Resolution Volume Discrepancy External Email - Use Caution Dear FreeSurfer Community, In processing high-resolution (0.7 mm^3 isotropic) and low resolution (1.0 mm^3 isotropic) versions of the same data we have received conflicting volume data in our aseg.stats file. Below is the relevant excerpt from those files. High-resolution (0.7 mm^3 isotropic) # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 3264609.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 3192286.00, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1330806.023066, mm^3 # Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 60940.00, mm^3 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 230160.306401, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 228696.462181, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 458856.768582, mm^3 # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 158718.858711, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 161112.395773, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 319831.254484, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 149905.00, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 941078.768582, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 970862.023066, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 909922.023066, mm^3 # Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 2790169.00, mm^3 # Measure Mask, MaskVol, Mask Volume, 4652001.00, mm^3 # Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 2.065785, unitless # Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 2.943701, unitless # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 46, unitless # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 70, unitless # Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 116, unitless # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1580323.941985, mm^3 Low resolution (1.0 mm^3 isotropic) # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1132377.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1107596.00, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1106786.650039, mm^3 # Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 21069.00, mm^3 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 226998.297110, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 225122.819041, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 452121.116151, mm^3 # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 228780.783147, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 235221.750741, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 464002.533888, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 51537.00, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 619358.116151, mm^3 # Measure SupraTentorial, SupraTento
