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, 3264609.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 3192286.000000, 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, 60940.000000, 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, 149905.000000, 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, 2790169.000000, mm^3 # Measure Mask, MaskVol, Mask Volume, 4652001.000000, 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, 1132377.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1107596.000000, 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, 21069.000000, 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, 51537.000000, 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, 968494.000000, mm^3 # Measure Mask, MaskVol, Mask Volume, 1574410.000000, 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 agreement. Others, like BrainSegVol, SubCortGrayVol and VentricleChoroidVol seem to be off by a factor of 0.7^3 = 0.343. Still others like TotalGrayVol and CerebralWhiteMatterVol seem to disagree in ways that are not obvious. The data are not shown but the subcortical gray matter volumes for specific areas seem to be in good agreement. The relevant function calls that were used to generate these files are:
recon-all -s <subj_id > <input_T1_file> -all -openmp 4 And the command I ran for the high-res (sub-mm) segmentation is recon-all -s <subj_id> <input_T1_file> -all -cm -expert expert.txt -openmp 4
And the content of expert.txt is just one line: mris_inflate -n 15
I wanted to ask if anyone could identify the source of these discrepancies, or how to resolve them. In particular I'm interested in how to resolve discrepancies in volumes which don't seem to be off by a scaling factor like TotalGrayVol.
Thank you very much! Gaurav Verma
External Email - Use Caution
Dear Gaurav Verma,
this should fix your issue: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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, 3264609.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 3192286.000000, 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, 60940.000000, 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, 149905.000000, 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, 2790169.000000, mm^3 # Measure Mask, MaskVol, Mask Volume, 4652001.000000, 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, 1132377.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1107596.000000, 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, 21069.000000, 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, 51537.000000, 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, 968494.000000, mm^3 # Measure Mask, MaskVol, Mask Volume, 1574410.000000, 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 agreement. Others, like BrainSegVol, SubCortGrayVol and VentricleChoroidVol seem to be off by a factor of 0.7^3 = 0.343. Still others like TotalGrayVol and CerebralWhiteMatterVol seem to disagree in ways that are not obvious. The data are not shown but the subcortical gray matter volumes for specific areas seem to be in good agreement. The relevant function calls that were used to generate these files are:
recon-all -s <subj_id > <input_T1_file> -all -openmp 4 And the command I ran for the high-res (sub-mm) segmentation is recon-all -s <subj_id> <input_T1_file> -all -cm -expert expert.txt -openmp 4
And the content of expert.txt is just one line: mris_inflate -n 15
I wanted to ask if anyone could identify the source of these discrepancies, or how to resolve them. In particular I'm interested in how to resolve discrepancies in volumes which don't seem to be off by a scaling factor like TotalGrayVol.
Thank you very much! Gaurav Verma
External Email - Use Caution
Thank you so much, Falk!
That addresses my concerns perfectly!
Gaurav
________________________________ From: falk.luesebrink@med.ovgu.de falk.luesebrink@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/BrainVolStatsFixedhttps://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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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, 3264609.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 3192286.000000, 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, 60940.000000, 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, 149905.000000, 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, 2790169.000000, mm^3 # Measure Mask, MaskVol, Mask Volume, 4652001.000000, 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, 1132377.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1107596.000000, 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, 21069.000000, 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, 51537.000000, 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, 968494.000000, mm^3 # Measure Mask, MaskVol, Mask Volume, 1574410.000000, 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 agreement. Others, like BrainSegVol, SubCortGrayVol and VentricleChoroidVol seem to be off by a factor of 0.7^3 = 0.343. Still others like TotalGrayVol and CerebralWhiteMatterVol seem to disagree in ways that are not obvious. The data are not shown but the subcortical gray matter volumes for specific areas seem to be in good agreement. The relevant function calls that were used to generate these files are:
recon-all -s <subj_id > <input_T1_file> -all -openmp 4 And the command I ran for the high-res (sub-mm) segmentation is recon-all -s <subj_id> <input_T1_file> -all -cm -expert expert.txt -openmp 4
And the content of expert.txt is just one line: mris_inflate -n 15
I wanted to ask if anyone could identify the source of these discrepancies, or how to resolve them. In particular I'm interested in how to resolve discrepancies in volumes which don't seem to be off by a scaling factor like TotalGrayVol.
Thank you very much! Gaurav Verma
freesurfer@nmr.mgh.harvard.edu
-
falk.luesebrink＠med.ovgu.de -
Verma, Gaurav