diff --git a/freesurfer_stats/__init__.py b/freesurfer_stats/__init__.py index 5a4e824..c96abbf 100644 --- a/freesurfer_stats/__init__.py +++ b/freesurfer_stats/__init__.py @@ -141,15 +141,16 @@ def _read(self, stream: typing.TextIO) -> None: self.whole_brain_measurements = pandas.DataFrame() line = self._read_header_line(stream) while not line.startswith('NTableCols'): - key, name, value, unit \ - = self._GENERAL_MEASUREMENTS_REGEX.match(line).groups() - if key == 'SupraTentorialVolNotVent' and name.lower() == 'supratentorial volume': - name += ' Without Ventricles' - column_name = self._format_column_name(name, unit) - assert column_name not in self.whole_brain_measurements, \ - (key, name, column_name, self.whole_brain_measurements) - self.whole_brain_measurements[column_name] \ - = pandas.to_numeric([value], errors='raise') + match = self._GENERAL_MEASUREMENTS_REGEX.match(line) + if match: + key, name, value, unit = match.groups() + if key == 'SupraTentorialVolNotVent' and name.lower() == 'supratentorial volume': + name += ' Without Ventricles' + column_name = self._format_column_name(name, unit) + assert column_name not in self.whole_brain_measurements, \ + (key, name, column_name, self.whole_brain_measurements) + self.whole_brain_measurements[column_name] \ + = pandas.to_numeric([value], errors='raise') line = self._read_header_line(stream) columns = self._read_column_attributes( int(line[len('NTableCols '):]), stream) diff --git a/tests/subjects/soichi/stats/aseg.stats b/tests/subjects/soichi/stats/aseg.stats new file mode 100644 index 0000000..13b754d --- /dev/null +++ b/tests/subjects/soichi/stats/aseg.stats @@ -0,0 +1,124 @@ +# Title Segmentation Statistics +# +# generating_program mri_segstats +# cvs_version 7.0.0 +# cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject output +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# anatomy_type volume +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# subjectname output +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000, mm^3 +# Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 9296.000000, mm^3 +# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 232345.220912, mm^3 +# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 222242.475246, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696158, mm^3 +# Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 251589.500000, mm^3 +# Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 244895.500000, mm^3 +# Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 496485.000000, mm^3 +# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 62428.000000, mm^3 +# Measure TotalGray, TotalGrayVol, Total gray matter volume, 625759.696158, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000, mm^3 +# Measure Mask, MaskVol, Mask Volume, 1686052.000000, mm^3 +# Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 0.823275, unitless +# Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 1.186998, unitless +# Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 24, unitless +# Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 25, unitless +# Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 49, unitless +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# SegVolFile mri/aseg.mgz +# SegVolFileTimeStamp 2020/05/04 22:14:04 +# ColorTable /usr/local/freesurfer/ASegStatsLUT.txt +# ColorTableTimeStamp 2020/04/29 22:19:19 +# InVolFile mri/norm.mgz +# InVolFileTimeStamp 2020/05/04 19:28:46 +# InVolFrame 0 +# PVVolFile mri/norm.mgz +# PVVolFileTimeStamp 2020/05/04 19:28:46 +# Excluding Cortical Gray and White Matter +# ExcludeSegId 0 2 3 41 42 +# VoxelVolume_mm3 1 +# TableCol 1 ColHeader Index +# TableCol 1 FieldName Index +# TableCol 1 Units NA +# TableCol 2 ColHeader SegId +# TableCol 2 FieldName Segmentation Id +# TableCol 2 Units NA +# TableCol 3 ColHeader NVoxels +# TableCol 3 FieldName Number of Voxels +# TableCol 3 Units unitless +# TableCol 4 ColHeader Volume_mm3 +# TableCol 4 FieldName Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader StructName +# TableCol 5 FieldName Structure Name +# TableCol 5 Units NA +# TableCol 6 ColHeader normMean +# TableCol 6 FieldName Intensity normMean +# TableCol 6 Units MR +# TableCol 7 ColHeader normStdDev +# TableCol 7 FieldName Itensity normStdDev +# TableCol 7 Units MR +# TableCol 8 ColHeader normMin +# TableCol 8 FieldName Intensity normMin +# TableCol 8 Units MR +# TableCol 9 ColHeader normMax +# TableCol 9 FieldName Intensity normMax +# TableCol 9 Units MR +# TableCol 10 ColHeader normRange +# TableCol 10 FieldName Intensity normRange +# TableCol 10 Units MR +# NRows 45 +# NTableCols 10 +# ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange + 1 4 5077 5581.1 Left-Lateral-Ventricle 27.3055 15.4437 0.0000 88.0000 88.0000 + 2 5 132 195.5 Left-Inf-Lat-Vent 53.1970 9.2625 37.0000 76.0000 39.0000 + 3 7 18074 18350.4 Left-Cerebellum-White-Matter 80.1782 9.0470 36.0000 106.0000 70.0000 + 4 8 54976 55868.4 Left-Cerebellum-Cortex 48.4004 10.9809 6.0000 98.0000 92.0000 + 5 10 8612 8178.8 Left-Thalamus 83.3560 10.4341 27.0000 114.0000 87.0000 + 6 11 3824 3708.7 Left-Caudate 70.4786 9.3153 30.0000 99.0000 69.0000 + 7 12 5776 5622.3 Left-Putamen 83.7332 7.1692 43.0000 102.0000 59.0000 + 8 13 2124 2091.0 Left-Pallidum 97.9812 3.8737 79.0000 110.0000 31.0000 + 9 14 679 741.0 3rd-Ventricle 37.1487 15.2063 0.0000 78.0000 78.0000 + 10 15 875 1019.4 4th-Ventricle 31.0811 14.2070 0.0000 76.0000 76.0000 + 11 16 21320 21011.7 Brain-Stem 84.7268 12.0079 25.0000 140.0000 115.0000 + 12 17 4357 4333.5 Left-Hippocampus 65.6167 8.2438 26.0000 108.0000 82.0000 + 13 18 1573 1549.1 Left-Amygdala 64.1742 6.3122 41.0000 83.0000 42.0000 + 14 24 965 1007.5 CSF 41.3772 12.8093 6.0000 68.0000 62.0000 + 15 26 731 718.7 Left-Accumbens-area 66.7989 5.7314 42.0000 86.0000 44.0000 + 16 28 4324 4125.1 Left-VentralDC 91.7333 12.2516 31.0000 132.0000 101.0000 + 17 30 0 0.0 Left-vessel 0.0000 0.0000 0.0000 0.0000 0.0000 + 18 31 419 356.7 Left-choroid-plexus 51.7375 15.3314 20.0000 80.0000 60.0000 + 19 43 3051 3370.2 Right-Lateral-Ventricle 35.5257 16.2240 0.0000 81.0000 81.0000 + 20 44 186 270.7 Right-Inf-Lat-Vent 46.6720 11.2473 14.0000 78.0000 64.0000 + 21 46 18717 19204.9 Right-Cerebellum-White-Matter 79.0736 9.2274 32.0000 106.0000 74.0000 + 22 47 53768 54076.3 Right-Cerebellum-Cortex 47.0445 10.8816 10.0000 92.0000 82.0000 + 23 49 7812 7387.3 Right-Thalamus 80.6749 9.9149 37.0000 103.0000 66.0000 + 24 50 3740 3580.3 Right-Caudate 73.5816 9.0473 37.0000 105.0000 68.0000 + 25 51 6114 5882.7 Right-Putamen 82.4882 7.7199 62.0000 122.0000 60.0000 + 26 52 2201 2163.7 Right-Pallidum 97.5766 3.9017 78.0000 108.0000 30.0000 + 27 53 4391 4328.9 Right-Hippocampus 65.4297 8.8955 25.0000 120.0000 95.0000 + 28 54 1715 1665.5 Right-Amygdala 63.4548 7.4180 31.0000 84.0000 53.0000 + 29 58 751 700.3 Right-Accumbens-area 68.9933 6.9871 49.0000 93.0000 44.0000 + 30 60 4383 4158.7 Right-VentralDC 88.2469 12.5069 35.0000 131.0000 96.0000 + 31 62 0 0.0 Right-vessel 0.0000 0.0000 0.0000 0.0000 0.0000 + 32 63 431 389.1 Right-choroid-plexus 54.3295 13.1272 26.0000 80.0000 54.0000 + 33 72 0 0.0 5th-Ventricle 0.0000 0.0000 0.0000 0.0000 0.0000 + 34 77 2244 1880.1 WM-hypointensities 69.7460 12.6019 33.0000 102.0000 69.0000 + 35 78 0 0.0 Left-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 + 36 79 0 0.0 Right-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 + 37 80 0 0.0 non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 + 38 81 0 0.0 Left-non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 + 39 82 0 0.0 Right-non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 + 40 85 152 139.0 Optic-Chiasm 67.6645 10.3527 42.0000 107.0000 65.0000 + 41 251 1297 1197.2 CC_Posterior 98.0948 12.6156 45.0000 113.0000 68.0000 + 42 252 707 631.7 CC_Mid_Posterior 89.1471 17.0599 20.0000 115.0000 95.0000 + 43 253 886 789.6 CC_Central 90.2009 16.9791 24.0000 119.0000 95.0000 + 44 254 905 809.6 CC_Mid_Anterior 93.8497 17.3849 32.0000 127.0000 95.0000 + 45 255 1192 1124.7 CC_Anterior 102.1720 12.2017 47.0000 126.0000 79.0000 diff --git a/tests/subjects/soichi/stats/brainvol.stats b/tests/subjects/soichi/stats/brainvol.stats new file mode 100644 index 0000000..4c0d0dd --- /dev/null +++ b/tests/subjects/soichi/stats/brainvol.stats @@ -0,0 +1,16 @@ +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000000000, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000000000, mm^3 +# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 62428.000000000000, mm^3 +# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 232345.220911918441, mm^3 +# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 222242.475245694164, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696157612605, mm^3 +# Measure TotalGray, TotalGrayVol, Total gray matter volume, 625759.696157612605, mm^3 +# Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 251589.500000000000, mm^3 +# Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 244895.500000000000, mm^3 +# Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 496485.000000000000, mm^3 +# Measure Mask, MaskVol, Mask Volume, 1686052.000000000000, mm^3 +# Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 1012058.000000000000, mm^3 +# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1157593.000000000000, mm^3 +# Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 9296.000000000000, mm^3 diff --git a/tests/subjects/soichi/stats/lh.BA_exvivo.stats b/tests/subjects/soichi/stats/lh.BA_exvivo.stats new file mode 100644 index 0000000..9b5f79e --- /dev/null +++ b/tests/subjects/soichi/stats/lh.BA_exvivo.stats @@ -0,0 +1,74 @@ +# Table of FreeSurfer cortical parcellation anatomical statistics +# +# CreationTime 2020/05/04-22:22:50-GMT +# generating_program mris_anatomical_stats +# cvs_version 7.0.0 +# mrisurf.c-cvs_version 7.0.0 +# cmdline mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab output lh white +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# anatomy_type surface +# subjectname output +# hemi lh +# AnnotationFile ./lh.BA_exvivo.annot +# AnnotationFileTimeStamp 2020/05/04 22:22:46 +# Measure Cortex, NumVert, Number of Vertices, 127765, unitless +# Measure Cortex, WhiteSurfArea, White Surface Total Area, 90204.3, mm^2 +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000, mm^3 +# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1157593.000000, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696158, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000, mm^3 +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# NTableCols 10 +# TableCol 1 ColHeader StructName +# TableCol 1 FieldName Structure Name +# TableCol 1 Units NA +# TableCol 2 ColHeader NumVert +# TableCol 2 FieldName Number of Vertices +# TableCol 2 Units unitless +# TableCol 3 ColHeader SurfArea +# TableCol 3 FieldName Surface Area +# TableCol 3 Units mm^2 +# TableCol 4 ColHeader GrayVol +# TableCol 4 FieldName Gray Matter Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader ThickAvg +# TableCol 5 FieldName Average Thickness +# TableCol 5 Units mm +# TableCol 6 ColHeader ThickStd +# TableCol 6 FieldName Thickness StdDev +# TableCol 6 Units mm +# TableCol 7 ColHeader MeanCurv +# TableCol 7 FieldName Integrated Rectified Mean Curvature +# TableCol 7 Units mm^-1 +# TableCol 8 ColHeader GausCurv +# TableCol 8 FieldName Integrated Rectified Gaussian Curvature +# TableCol 8 Units mm^-2 +# TableCol 9 ColHeader FoldInd +# TableCol 9 FieldName Folding Index +# TableCol 9 Units unitless +# TableCol 10 ColHeader CurvInd +# TableCol 10 FieldName Intrinsic Curvature Index +# TableCol 10 Units unitless +# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd +BA1_exvivo 1091 779 2228 2.233 0.587 0.140 0.032 13 1.5 +BA2_exvivo 3956 2761 6357 2.112 0.581 0.126 0.027 39 4.4 +BA3a_exvivo 1132 726 973 1.785 0.396 0.129 0.028 10 1.3 +BA3b_exvivo 2250 1572 3226 1.811 0.557 0.112 0.025 18 2.3 +BA4a_exvivo 1849 1082 3167 2.671 0.626 0.099 0.022 11 1.7 +BA4p_exvivo 1313 932 1786 2.033 0.504 0.116 0.026 8 1.5 +BA6_exvivo 10247 6816 22620 2.873 0.634 0.111 0.023 82 9.7 +BA44_exvivo 2571 1892 5119 2.394 0.596 0.121 0.024 25 2.8 +BA45_exvivo 2876 2112 6879 2.597 0.807 0.131 0.033 30 4.0 +V1_exvivo 3587 2681 4840 1.791 0.478 0.151 0.039 45 5.8 +V2_exvivo 7987 5971 13181 2.067 0.540 0.155 0.039 108 13.2 +MT_exvivo 1812 1342 3308 2.268 0.545 0.140 0.032 21 2.5 +perirhinal_exvivo 572 418 1747 3.036 0.856 0.115 0.031 5 0.8 +entorhinal_exvivo 544 350 1553 2.938 1.298 0.109 0.032 6 0.7 diff --git a/tests/subjects/soichi/stats/lh.BA_exvivo.thresh.stats b/tests/subjects/soichi/stats/lh.BA_exvivo.thresh.stats new file mode 100644 index 0000000..0c05805 --- /dev/null +++ b/tests/subjects/soichi/stats/lh.BA_exvivo.thresh.stats @@ -0,0 +1,74 @@ +# Table of FreeSurfer cortical parcellation anatomical statistics +# +# CreationTime 2020/05/04-22:22:54-GMT +# generating_program mris_anatomical_stats +# cvs_version 7.0.0 +# mrisurf.c-cvs_version 7.0.0 +# cmdline mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab output lh white +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# anatomy_type surface +# subjectname output +# hemi lh +# AnnotationFile ./lh.BA_exvivo.thresh.annot +# AnnotationFileTimeStamp 2020/05/04 22:22:46 +# Measure Cortex, NumVert, Number of Vertices, 127765, unitless +# Measure Cortex, WhiteSurfArea, White Surface Total Area, 90204.3, mm^2 +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000, mm^3 +# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1157593.000000, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696158, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000, mm^3 +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# NTableCols 10 +# TableCol 1 ColHeader StructName +# TableCol 1 FieldName Structure Name +# TableCol 1 Units NA +# TableCol 2 ColHeader NumVert +# TableCol 2 FieldName Number of Vertices +# TableCol 2 Units unitless +# TableCol 3 ColHeader SurfArea +# TableCol 3 FieldName Surface Area +# TableCol 3 Units mm^2 +# TableCol 4 ColHeader GrayVol +# TableCol 4 FieldName Gray Matter Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader ThickAvg +# TableCol 5 FieldName Average Thickness +# TableCol 5 Units mm +# TableCol 6 ColHeader ThickStd +# TableCol 6 FieldName Thickness StdDev +# TableCol 6 Units mm +# TableCol 7 ColHeader MeanCurv +# TableCol 7 FieldName Integrated Rectified Mean Curvature +# TableCol 7 Units mm^-1 +# TableCol 8 ColHeader GausCurv +# TableCol 8 FieldName Integrated Rectified Gaussian Curvature +# TableCol 8 Units mm^-2 +# TableCol 9 ColHeader FoldInd +# TableCol 9 FieldName Folding Index +# TableCol 9 Units unitless +# TableCol 10 ColHeader CurvInd +# TableCol 10 FieldName Intrinsic Curvature Index +# TableCol 10 Units unitless +# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd +BA1_exvivo 715 485 1423 2.282 0.614 0.132 0.029 7 0.8 +BA2_exvivo 1731 1199 3078 2.154 0.627 0.123 0.026 17 1.9 +BA3a_exvivo 979 622 789 1.771 0.391 0.131 0.027 9 1.1 +BA3b_exvivo 1429 963 1633 1.619 0.335 0.090 0.016 7 0.9 +BA4a_exvivo 1803 1098 2994 2.554 0.655 0.102 0.022 11 1.6 +BA4p_exvivo 1048 744 1373 2.059 0.481 0.121 0.030 6 1.4 +BA6_exvivo 5756 3660 12361 2.914 0.616 0.106 0.022 42 5.2 +BA44_exvivo 1629 1194 3329 2.408 0.587 0.121 0.026 17 1.8 +BA45_exvivo 1146 896 3419 2.891 0.861 0.149 0.043 16 2.0 +V1_exvivo 3798 2857 5268 1.803 0.480 0.153 0.040 50 6.4 +V2_exvivo 3980 3033 6335 1.981 0.519 0.161 0.042 58 7.2 +MT_exvivo 503 392 845 2.043 0.515 0.146 0.029 7 0.8 +perirhinal_exvivo 234 157 525 2.888 0.857 0.077 0.022 1 0.2 +entorhinal_exvivo 332 210 1129 3.495 0.665 0.063 0.011 1 0.1 diff --git a/tests/subjects/soichi/stats/lh.aparc.DKTatlas.stats b/tests/subjects/soichi/stats/lh.aparc.DKTatlas.stats new file mode 100644 index 0000000..021badc --- /dev/null +++ b/tests/subjects/soichi/stats/lh.aparc.DKTatlas.stats @@ -0,0 +1,92 @@ +# Table of FreeSurfer cortical parcellation anatomical statistics +# +# CreationTime 2020/05/04-22:20:53-GMT +# generating_program mris_anatomical_stats +# cvs_version 7.0.0 +# mrisurf.c-cvs_version 7.0.0 +# cmdline mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab output lh white +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# anatomy_type surface +# subjectname output +# hemi lh +# AnnotationFile ../label/lh.aparc.DKTatlas.annot +# AnnotationFileTimeStamp 2020/05/04 22:13:39 +# Measure Cortex, NumVert, Number of Vertices, 118968, unitless +# Measure Cortex, WhiteSurfArea, White Surface Total Area, 84858.5, mm^2 +# Measure Cortex, MeanThickness, Mean Thickness, 2.39891, mm +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000, mm^3 +# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1157593.000000, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696158, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000, mm^3 +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# NTableCols 10 +# TableCol 1 ColHeader StructName +# TableCol 1 FieldName Structure Name +# TableCol 1 Units NA +# TableCol 2 ColHeader NumVert +# TableCol 2 FieldName Number of Vertices +# TableCol 2 Units unitless +# TableCol 3 ColHeader SurfArea +# TableCol 3 FieldName Surface Area +# TableCol 3 Units mm^2 +# TableCol 4 ColHeader GrayVol +# TableCol 4 FieldName Gray Matter Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader ThickAvg +# TableCol 5 FieldName Average Thickness +# TableCol 5 Units mm +# TableCol 6 ColHeader ThickStd +# TableCol 6 FieldName Thickness StdDev +# TableCol 6 Units mm +# TableCol 7 ColHeader MeanCurv +# TableCol 7 FieldName Integrated Rectified Mean Curvature +# TableCol 7 Units mm^-1 +# TableCol 8 ColHeader GausCurv +# TableCol 8 FieldName Integrated Rectified Gaussian Curvature +# TableCol 8 Units mm^-2 +# TableCol 9 ColHeader FoldInd +# TableCol 9 FieldName Folding Index +# TableCol 9 Units unitless +# TableCol 10 ColHeader CurvInd +# TableCol 10 FieldName Intrinsic Curvature Index +# TableCol 10 Units unitless +# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd +caudalanteriorcingulate 1913 1239 3603 2.467 0.703 0.115 0.017 16 1.3 +caudalmiddlefrontal 3919 2699 7488 2.496 0.570 0.114 0.022 31 3.6 +cuneus 3305 2371 4814 1.980 0.503 0.137 0.030 37 4.2 +entorhinal 508 320 1421 3.022 0.865 0.079 0.018 2 0.3 +fusiform 3482 2583 6723 2.345 0.635 0.145 0.036 44 5.4 +inferiorparietal 5860 4275 11468 2.368 0.575 0.135 0.030 62 7.5 +inferiortemporal 3641 2785 8483 2.357 0.773 0.142 0.037 49 6.0 +isthmuscingulate 1531 1046 2524 2.232 0.606 0.128 0.029 17 2.0 +lateraloccipital 7076 5131 11714 2.097 0.545 0.145 0.035 86 10.6 +lateralorbitofrontal 3893 2821 9107 2.833 0.824 0.139 0.039 51 6.6 +lingual 4323 3349 7887 2.156 0.590 0.157 0.042 59 7.6 +medialorbitofrontal 2379 1656 5771 2.765 0.957 0.115 0.031 25 3.1 +middletemporal 4629 3479 8935 2.105 0.644 0.135 0.035 55 6.9 +parahippocampal 852 543 1868 2.887 0.823 0.091 0.020 5 0.6 +paracentral 2855 1759 5288 2.739 0.600 0.098 0.020 17 2.3 +parsopercularis 2322 1661 4742 2.547 0.600 0.118 0.025 21 2.4 +parsorbitalis 1035 709 2200 2.608 0.616 0.113 0.027 8 1.1 +parstriangularis 2403 1731 5599 2.663 0.795 0.126 0.029 23 3.0 +pericalcarine 2055 1502 2258 1.689 0.367 0.147 0.036 25 3.2 +postcentral 7197 4984 11417 2.064 0.617 0.123 0.027 68 8.3 +posteriorcingulate 2075 1381 3661 2.363 0.689 0.125 0.025 22 2.2 +precentral 7814 5201 13250 2.396 0.634 0.116 0.025 64 8.6 +precuneus 4726 3356 8727 2.345 0.536 0.125 0.027 47 5.0 +rostralanteriorcingulate 1884 1351 3455 2.252 0.736 0.139 0.039 27 3.3 +rostralmiddlefrontal 5163 3950 11914 2.420 0.696 0.150 0.044 69 9.9 +superiorfrontal 11464 8188 28745 2.914 0.726 0.127 0.031 108 14.7 +superiorparietal 5153 3626 8404 2.165 0.512 0.126 0.026 51 5.5 +superiortemporal 7014 4942 14435 2.457 0.688 0.117 0.026 64 8.2 +supramarginal 4962 3772 9689 2.178 0.601 0.144 0.035 66 7.7 +transversetemporal 788 562 1626 2.337 0.591 0.139 0.047 10 1.8 +insula 2747 1886 5438 2.826 0.692 0.116 0.027 21 2.9 diff --git a/tests/subjects/soichi/stats/lh.aparc.a2009s.stats b/tests/subjects/soichi/stats/lh.aparc.a2009s.stats new file mode 100644 index 0000000..98d531f --- /dev/null +++ b/tests/subjects/soichi/stats/lh.aparc.a2009s.stats @@ -0,0 +1,135 @@ +# Table of FreeSurfer cortical parcellation anatomical statistics +# +# CreationTime 2020/05/04-22:20:40-GMT +# generating_program mris_anatomical_stats +# cvs_version 7.0.0 +# mrisurf.c-cvs_version 7.0.0 +# cmdline mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab output lh white +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# anatomy_type surface +# subjectname output +# hemi lh +# AnnotationFile ../label/lh.aparc.a2009s.annot +# AnnotationFileTimeStamp 2020/05/04 22:13:27 +# Measure Cortex, NumVert, Number of Vertices, 118968, unitless +# Measure Cortex, WhiteSurfArea, White Surface Total Area, 84858.5, mm^2 +# Measure Cortex, MeanThickness, Mean Thickness, 2.39891, mm +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000, mm^3 +# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1157593.000000, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696158, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000, mm^3 +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# NTableCols 10 +# TableCol 1 ColHeader StructName +# TableCol 1 FieldName Structure Name +# TableCol 1 Units NA +# TableCol 2 ColHeader NumVert +# TableCol 2 FieldName Number of Vertices +# TableCol 2 Units unitless +# TableCol 3 ColHeader SurfArea +# TableCol 3 FieldName Surface Area +# TableCol 3 Units mm^2 +# TableCol 4 ColHeader GrayVol +# TableCol 4 FieldName Gray Matter Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader ThickAvg +# TableCol 5 FieldName Average Thickness +# TableCol 5 Units mm +# TableCol 6 ColHeader ThickStd +# TableCol 6 FieldName Thickness StdDev +# TableCol 6 Units mm +# TableCol 7 ColHeader MeanCurv +# TableCol 7 FieldName Integrated Rectified Mean Curvature +# TableCol 7 Units mm^-1 +# TableCol 8 ColHeader GausCurv +# TableCol 8 FieldName Integrated Rectified Gaussian Curvature +# TableCol 8 Units mm^-2 +# TableCol 9 ColHeader FoldInd +# TableCol 9 FieldName Folding Index +# TableCol 9 Units unitless +# TableCol 10 ColHeader CurvInd +# TableCol 10 FieldName Intrinsic Curvature Index +# TableCol 10 Units unitless +# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd +G_and_S_frontomargin 938 721 2753 3.043 0.902 0.155 0.049 13 1.6 +G_and_S_occipital_inf 1521 1161 3032 2.297 0.544 0.147 0.032 19 2.1 +G_and_S_paracentral 1819 1111 3167 2.483 0.627 0.102 0.021 13 1.5 +G_and_S_subcentral 1560 1189 3029 2.259 0.591 0.146 0.034 19 2.4 +G_and_S_transv_frontopol 697 581 2663 3.084 0.849 0.193 0.061 13 1.9 +G_and_S_cingul-Ant 2242 1586 4187 2.381 0.694 0.124 0.031 22 3.0 +G_and_S_cingul-Mid-Ant 1426 934 2344 2.515 0.745 0.103 0.014 9 0.8 +G_and_S_cingul-Mid-Post 1431 940 2497 2.486 0.622 0.109 0.022 12 1.4 +G_cingul-Post-dorsal 561 405 1498 2.797 0.658 0.153 0.041 8 0.9 +G_cingul-Post-ventral 317 216 734 2.549 0.661 0.120 0.026 4 0.4 +G_cuneus 2292 1701 3582 1.872 0.451 0.155 0.037 29 3.8 +G_front_inf-Opercular 1255 974 3278 2.579 0.625 0.139 0.035 18 1.8 +G_front_inf-Orbital 472 333 1358 2.755 0.619 0.145 0.040 6 0.9 +G_front_inf-Triangul 1161 909 3632 3.013 0.778 0.150 0.039 16 1.9 +G_front_middle 4081 3199 11487 2.588 0.687 0.157 0.043 63 7.8 +G_front_sup 7937 5531 22110 3.060 0.703 0.127 0.030 76 10.1 +G_Ins_lg_and_S_cent_ins 662 480 1396 2.928 0.855 0.135 0.033 8 0.9 +G_insular_short 669 476 2039 3.162 0.869 0.136 0.041 7 1.1 +G_occipital_middle 1857 1419 4488 2.490 0.509 0.161 0.042 27 3.4 +G_occipital_sup 1183 881 2029 1.974 0.482 0.153 0.035 17 1.7 +G_oc-temp_lat-fusifor 1368 1052 3428 2.581 0.658 0.160 0.046 21 2.7 +G_oc-temp_med-Lingual 2796 2216 5713 2.207 0.663 0.172 0.050 47 5.9 +G_oc-temp_med-Parahip 1073 678 2803 2.998 0.860 0.096 0.023 7 0.8 +G_orbital 2234 1760 6277 2.728 0.684 0.166 0.051 42 5.3 +G_pariet_inf-Angular 2139 1674 5707 2.581 0.612 0.156 0.038 31 3.5 +G_pariet_inf-Supramar 2825 2258 6716 2.243 0.694 0.160 0.042 48 5.5 +G_parietal_sup 2235 1657 4450 2.282 0.557 0.147 0.032 30 3.0 +G_postcentral 2512 1776 4778 2.161 0.660 0.138 0.032 29 3.5 +G_precentral 2966 1876 6162 2.628 0.670 0.113 0.027 25 3.3 +G_precuneus 2103 1556 5141 2.494 0.589 0.146 0.035 29 2.9 +G_rectus 941 693 2466 2.614 0.722 0.139 0.038 15 1.6 +G_subcallosal 877 582 1530 2.534 0.836 0.127 0.048 10 1.7 +G_temp_sup-G_T_transv 690 492 1620 2.397 0.629 0.154 0.054 10 1.8 +G_temp_sup-Lateral 1823 1404 5045 2.597 0.729 0.149 0.038 26 3.1 +G_temp_sup-Plan_polar 874 582 1791 2.649 0.695 0.073 0.012 2 0.5 +G_temp_sup-Plan_tempo 762 557 1401 2.168 0.622 0.113 0.032 8 1.2 +G_temporal_inf 1798 1449 4678 2.383 0.752 0.157 0.045 30 3.7 +G_temporal_middle 1961 1600 5158 2.247 0.720 0.157 0.049 33 4.2 +Lat_Fis-ant-Horizont 348 226 457 2.309 0.391 0.076 0.011 2 0.1 +Lat_Fis-ant-Vertical 384 250 494 2.274 0.592 0.097 0.021 2 0.3 +Lat_Fis-post 1147 772 1352 2.229 0.415 0.117 0.023 8 1.2 +Pole_occipital 1824 1364 2907 1.927 0.510 0.149 0.040 25 2.9 +Pole_temporal 1554 1236 5094 2.721 0.865 0.150 0.037 23 2.7 +S_calcarine 2776 2018 3383 1.881 0.470 0.133 0.032 27 3.6 +S_central 3209 2141 3334 1.823 0.437 0.111 0.023 21 3.1 +S_cingul-Marginalis 1179 776 1716 2.411 0.545 0.103 0.017 7 0.7 +S_circular_insula_ant 549 361 742 2.638 0.564 0.101 0.018 2 0.5 +S_circular_insula_inf 1325 854 1792 2.531 0.559 0.085 0.015 5 0.8 +S_circular_insula_sup 1722 1146 2722 2.793 0.527 0.108 0.021 9 1.6 +S_collat_transv_ant 882 635 1533 2.382 0.690 0.132 0.028 11 1.2 +S_collat_transv_post 526 366 570 1.949 0.355 0.153 0.035 6 0.8 +S_front_inf 2376 1606 3538 2.285 0.589 0.108 0.023 15 2.1 +S_front_middle 1266 876 1878 2.299 0.701 0.117 0.030 9 1.5 +S_front_sup 2988 2055 4995 2.501 0.508 0.099 0.023 16 2.7 +S_interm_prim-Jensen 341 231 412 2.065 0.486 0.141 0.036 3 0.5 +S_intrapariet_and_P_trans 2417 1640 3220 2.146 0.480 0.107 0.020 16 2.0 +S_oc_middle_and_Lunatus 1244 851 1419 1.969 0.460 0.131 0.030 10 1.6 +S_oc_sup_and_transversal 1388 931 1657 1.924 0.396 0.117 0.021 10 1.3 +S_occipital_ant 667 448 735 1.990 0.342 0.122 0.027 6 0.7 +S_oc-temp_lat 586 387 765 2.177 0.470 0.121 0.026 4 0.7 +S_oc-temp_med_and_Lingual 2043 1443 2810 2.084 0.551 0.121 0.025 17 2.0 +S_orbital_lateral 241 161 271 1.891 0.354 0.105 0.013 1 0.1 +S_orbital_med-olfact 640 420 835 2.487 0.802 0.099 0.016 4 0.4 +S_orbital-H_Shaped 1227 836 2452 2.883 0.874 0.121 0.031 11 1.8 +S_parieto_occipital 2426 1655 3367 2.265 0.509 0.106 0.020 17 2.0 +S_pericallosal 1373 897 1341 1.876 0.477 0.141 0.024 21 1.4 +S_postcentral 2934 2003 3886 2.004 0.472 0.117 0.023 25 2.8 +S_precentral-inf-part 1991 1337 3066 2.405 0.543 0.099 0.017 12 1.5 +S_precentral-sup-part 1470 989 2153 2.419 0.477 0.104 0.018 9 1.1 +S_suborbital 713 455 1700 3.106 1.137 0.083 0.012 3 0.3 +S_subparietal 855 579 1150 2.107 0.416 0.126 0.026 7 0.9 +S_temporal_inf 1257 840 1450 1.885 0.601 0.109 0.021 7 1.0 +S_temporal_sup 4611 3181 6805 2.206 0.530 0.113 0.023 33 4.2 +S_temporal_transverse 431 281 485 2.060 0.424 0.089 0.010 2 0.2 diff --git a/tests/subjects/soichi/stats/lh.aparc.pial.stats b/tests/subjects/soichi/stats/lh.aparc.pial.stats new file mode 100644 index 0000000..faa3cc7 --- /dev/null +++ b/tests/subjects/soichi/stats/lh.aparc.pial.stats @@ -0,0 +1,95 @@ +# Table of FreeSurfer cortical parcellation anatomical statistics +# +# CreationTime 2020/05/04-22:20:27-GMT +# generating_program mris_anatomical_stats +# cvs_version 7.0.0 +# mrisurf.c-cvs_version 7.0.0 +# cmdline mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab output lh pial +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# anatomy_type surface +# subjectname output +# hemi lh +# AnnotationFile ../label/lh.aparc.annot +# AnnotationFileTimeStamp 2020/05/04 21:58:14 +# Measure Cortex, NumVert, Number of Vertices, 118968, unitless +# Measure Cortex, PialSurfArea, Pial Surface Total Area, 109814, mm^2 +# Measure Cortex, MeanThickness, Mean Thickness, 2.39891, mm +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000, mm^3 +# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1157593.000000, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696158, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000, mm^3 +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# NTableCols 10 +# TableCol 1 ColHeader StructName +# TableCol 1 FieldName Structure Name +# TableCol 1 Units NA +# TableCol 2 ColHeader NumVert +# TableCol 2 FieldName Number of Vertices +# TableCol 2 Units unitless +# TableCol 3 ColHeader SurfArea +# TableCol 3 FieldName Surface Area +# TableCol 3 Units mm^2 +# TableCol 4 ColHeader GrayVol +# TableCol 4 FieldName Gray Matter Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader ThickAvg +# TableCol 5 FieldName Average Thickness +# TableCol 5 Units mm +# TableCol 6 ColHeader ThickStd +# TableCol 6 FieldName Thickness StdDev +# TableCol 6 Units mm +# TableCol 7 ColHeader MeanCurv +# TableCol 7 FieldName Integrated Rectified Mean Curvature +# TableCol 7 Units mm^-1 +# TableCol 8 ColHeader GausCurv +# TableCol 8 FieldName Integrated Rectified Gaussian Curvature +# TableCol 8 Units mm^-2 +# TableCol 9 ColHeader FoldInd +# TableCol 9 FieldName Folding Index +# TableCol 9 Units unitless +# TableCol 10 ColHeader CurvInd +# TableCol 10 FieldName Intrinsic Curvature Index +# TableCol 10 Units unitless +# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd +bankssts 1069 724 1536 2.144 0.501 0.127 0.036 14 1.6 +caudalanteriorcingulate 861 650 1400 2.356 0.465 0.183 0.051 153 2.3 +caudalmiddlefrontal 3635 3004 6949 2.492 0.571 0.138 0.033 58 4.9 +cuneus 2419 2098 3546 1.954 0.480 0.150 0.039 48 3.7 +entorhinal 548 747 1673 3.053 0.883 0.292 0.086 19 2.2 +fusiform 3637 3637 7582 2.391 0.663 0.178 0.043 74 6.9 +inferiorparietal 5697 5287 11237 2.366 0.575 0.167 0.040 149 10.2 +inferiortemporal 3670 3858 7429 2.242 0.732 0.191 0.048 71 7.6 +isthmuscingulate 1534 1285 2524 2.216 0.610 0.187 0.057 74 3.8 +lateraloccipital 7117 6300 11787 2.107 0.541 0.153 0.038 268 11.8 +lateralorbitofrontal 3716 3386 7928 2.754 0.771 0.182 0.051 129 7.9 +lingual 4256 4271 7791 2.167 0.591 0.186 0.048 112 8.7 +medialorbitofrontal 2868 3015 6587 2.698 0.908 0.197 0.053 99 6.8 +middletemporal 3466 4545 7508 2.136 0.678 0.221 0.050 58 7.8 +parahippocampal 869 839 1942 2.905 0.822 0.183 0.051 12 2.0 +paracentral 2463 1803 4322 2.661 0.585 1.561 1.470 29914077 2.6 +parsopercularis 2485 2248 5018 2.506 0.609 0.165 0.041 38 4.5 +parsorbitalis 890 1203 2586 2.739 0.631 0.242 0.057 18 2.2 +parstriangularis 1980 1958 4688 2.743 0.784 0.184 0.048 34 4.3 +pericalcarine 2096 1362 2311 1.688 0.366 0.139 0.044 73 3.5 +postcentral 6436 5760 10430 2.050 0.626 0.152 0.036 87 9.7 +posteriorcingulate 1883 1586 3388 2.369 0.697 0.177 0.055 97 3.9 +precentral 8010 6061 13626 2.403 0.626 0.118 0.028 108 9.3 +precuneus 4973 4098 8876 2.349 0.519 0.146 0.039 79 7.8 +rostralanteriorcingulate 1336 1432 2452 2.138 0.702 0.221 0.061 86 3.7 +rostralmiddlefrontal 7137 7769 16971 2.507 0.744 0.200 0.048 186 15.3 +superiorfrontal 11318 10278 27120 2.894 0.733 0.153 0.039 185 17.8 +superiorparietal 6602 5359 10653 2.128 0.536 0.145 0.035 110 9.4 +superiortemporal 5500 5099 10626 2.377 0.641 0.171 0.048 118 11.1 +supramarginal 5498 5489 10599 2.190 0.598 0.182 0.044 105 10.6 +frontalpole 310 451 1203 3.167 1.032 0.242 0.054 5 0.7 +temporalpole 717 1082 2427 3.027 0.807 0.247 0.057 16 2.0 +transversetemporal 757 860 1589 2.368 0.586 0.200 0.054 8 1.8 +insula 3215 2269 6352 2.897 0.721 0.173 0.064 199 7.6 diff --git a/tests/subjects/soichi/stats/lh.aparc.stats b/tests/subjects/soichi/stats/lh.aparc.stats new file mode 100644 index 0000000..48e1ed2 --- /dev/null +++ b/tests/subjects/soichi/stats/lh.aparc.stats @@ -0,0 +1,95 @@ +# Table of FreeSurfer cortical parcellation anatomical statistics +# +# CreationTime 2020/05/04-22:20:26-GMT +# generating_program mris_anatomical_stats +# cvs_version 7.0.0 +# mrisurf.c-cvs_version 7.0.0 +# cmdline mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab output lh white +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# anatomy_type surface +# subjectname output +# hemi lh +# AnnotationFile ../label/lh.aparc.annot +# AnnotationFileTimeStamp 2020/05/04 21:58:14 +# Measure Cortex, NumVert, Number of Vertices, 118968, unitless +# Measure Cortex, WhiteSurfArea, White Surface Total Area, 84858.5, mm^2 +# Measure Cortex, MeanThickness, Mean Thickness, 2.39891, mm +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000, mm^3 +# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1157593.000000, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696158, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000, mm^3 +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# NTableCols 10 +# TableCol 1 ColHeader StructName +# TableCol 1 FieldName Structure Name +# TableCol 1 Units NA +# TableCol 2 ColHeader NumVert +# TableCol 2 FieldName Number of Vertices +# TableCol 2 Units unitless +# TableCol 3 ColHeader SurfArea +# TableCol 3 FieldName Surface Area +# TableCol 3 Units mm^2 +# TableCol 4 ColHeader GrayVol +# TableCol 4 FieldName Gray Matter Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader ThickAvg +# TableCol 5 FieldName Average Thickness +# TableCol 5 Units mm +# TableCol 6 ColHeader ThickStd +# TableCol 6 FieldName Thickness StdDev +# TableCol 6 Units mm +# TableCol 7 ColHeader MeanCurv +# TableCol 7 FieldName Integrated Rectified Mean Curvature +# TableCol 7 Units mm^-1 +# TableCol 8 ColHeader GausCurv +# TableCol 8 FieldName Integrated Rectified Gaussian Curvature +# TableCol 8 Units mm^-2 +# TableCol 9 ColHeader FoldInd +# TableCol 9 FieldName Folding Index +# TableCol 9 Units unitless +# TableCol 10 ColHeader CurvInd +# TableCol 10 FieldName Intrinsic Curvature Index +# TableCol 10 Units unitless +# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd +bankssts 1069 732 1536 2.144 0.501 0.109 0.021 7 1.0 +caudalanteriorcingulate 861 559 1400 2.356 0.465 0.123 0.015 9 0.5 +caudalmiddlefrontal 3635 2504 6949 2.492 0.571 0.114 0.022 29 3.4 +cuneus 2419 1740 3546 1.954 0.480 0.144 0.033 29 3.3 +entorhinal 548 357 1673 3.053 0.883 0.082 0.018 3 0.3 +fusiform 3637 2723 7582 2.391 0.663 0.147 0.037 50 5.9 +inferiorparietal 5697 4170 11237 2.366 0.575 0.134 0.030 60 7.1 +inferiortemporal 3670 2730 7429 2.242 0.732 0.138 0.034 44 5.4 +isthmuscingulate 1534 1043 2524 2.216 0.610 0.130 0.030 20 2.0 +lateraloccipital 7117 5176 11787 2.107 0.541 0.144 0.035 85 10.6 +lateralorbitofrontal 3716 2627 7928 2.754 0.771 0.132 0.034 45 5.7 +lingual 4256 3297 7791 2.167 0.591 0.159 0.043 59 7.9 +medialorbitofrontal 2868 1979 6587 2.698 0.908 0.112 0.029 28 3.2 +middletemporal 3466 2711 7508 2.136 0.678 0.142 0.039 47 5.8 +parahippocampal 869 557 1942 2.905 0.822 0.094 0.022 5 0.7 +paracentral 2463 1525 4322 2.661 0.585 0.102 0.019 15 2.0 +parsopercularis 2485 1775 5018 2.506 0.609 0.114 0.024 21 2.4 +parsorbitalis 890 704 2586 2.739 0.631 0.172 0.052 16 2.2 +parstriangularis 1980 1438 4688 2.743 0.784 0.126 0.029 19 2.4 +pericalcarine 2096 1524 2311 1.688 0.366 0.144 0.035 25 3.0 +postcentral 6436 4475 10430 2.050 0.626 0.122 0.026 61 7.3 +posteriorcingulate 1883 1261 3388 2.369 0.697 0.128 0.026 21 2.0 +precentral 8010 5324 13626 2.403 0.626 0.116 0.025 66 8.7 +precuneus 4973 3519 8876 2.349 0.519 0.124 0.026 46 5.3 +rostralanteriorcingulate 1336 981 2452 2.138 0.702 0.147 0.041 21 2.7 +rostralmiddlefrontal 7137 5404 16971 2.507 0.744 0.145 0.043 89 12.7 +superiorfrontal 11318 7858 27120 2.894 0.733 0.119 0.027 94 12.6 +superiorparietal 6602 4642 10653 2.128 0.536 0.128 0.027 67 7.2 +superiortemporal 5500 3857 10626 2.377 0.641 0.116 0.027 50 6.8 +supramarginal 5498 4140 10599 2.190 0.598 0.143 0.035 71 8.5 +frontalpole 310 264 1203 3.167 1.032 0.223 0.072 8 1.1 +temporalpole 717 540 2427 3.027 0.807 0.129 0.029 8 1.0 +transversetemporal 757 535 1589 2.368 0.586 0.122 0.035 8 1.1 +insula 3215 2187 6352 2.897 0.721 0.116 0.028 25 3.6 diff --git a/tests/subjects/soichi/stats/lh.curv.stats b/tests/subjects/soichi/stats/lh.curv.stats new file mode 100644 index 0000000..2f75da9 --- /dev/null +++ b/tests/subjects/soichi/stats/lh.curv.stats @@ -0,0 +1,220 @@ + +Raw +- (using 'lh.curv'): -0.02314 +- 0.1621 + Raw Min: -2.23337 at vertex 35075 + Raw Max: 1.19343 at vertex 68197 + Raw Curvature Calculation Type: discrete + Raw Mean Vertex Separation (Whole Surface): 0.85839 +- 0.14471 mm + Raw Total Surface Area: 80629.67188 mm^2 + Raw Total Number of Vertices: 127765 + Raw Average Vertex Area (Whole Surface): 0.63108 mm^2 + Raw Natural Surface Integral: -1984.53455 + Raw Rectified Surface Integral: 10314.14844 + Raw Positive Surface Integral: 4164.80664 + Raw Negative Surface Integral: 6149.34131 + Raw Mean Natural Surface Integral: -0.01553 across 127765 (100.00%) vertices + Raw Mean Rectified Surface Integral: 0.08073 across 127765 (100.00%) vertices + Raw Mean Positive Surface Integral: 0.06792 across 61323 (48.00%) vertices + Raw Mean Negative Surface Integral: 0.09255 across 66442 (52.00%) vertices + Raw AreaNorm Natural Surface Integral: -0.02461 across 80629.421875 (100.00%) mm^2 + Raw AreaNorm Rectified Surface Integral: 0.12792 across 80629.421875 (100.00%) mm^2 + Raw AreaNorm Positive Surface Integral: 0.11034 across 37744.648438 (46.81%) mm^2 + Raw AreaNorm Negative Surface Integral: 0.14339 across 42885.203125 (53.19%) mm^2 + +Raw +- (using 'lh.sulc'): 0.00000 +- 5.6515 + Raw Min: -13.69147 at vertex 73122 + Raw Max: 16.49734 at vertex 44539 + Raw Curvature Calculation Type: discrete + Raw Mean Vertex Separation (Whole Surface): 0.85839 +- 0.14471 mm + Raw Total Surface Area: 80629.67188 mm^2 + Raw Total Number of Vertices: 127765 + Raw Average Vertex Area (Whole Surface): 0.63108 mm^2 + Raw Natural Surface Integral: -11830.13184 + Raw Rectified Surface Integral: 372129.21875 + Raw Positive Surface Integral: 180149.53125 + Raw Negative Surface Integral: 191979.67188 + Raw Mean Natural Surface Integral: -0.09259 across 127765 (100.00%) vertices + Raw Mean Rectified Surface Integral: 2.91261 across 127765 (100.00%) vertices + Raw Mean Positive Surface Integral: 2.98706 across 60310 (47.20%) vertices + Raw Mean Negative Surface Integral: 2.84604 across 67455 (52.80%) vertices + Raw AreaNorm Natural Surface Integral: -0.14672 across 80629.421875 (100.00%) mm^2 + Raw AreaNorm Rectified Surface Integral: 4.61530 across 80629.421875 (100.00%) mm^2 + Raw AreaNorm Positive Surface Integral: 4.86481 across 37031.179688 (45.93%) mm^2 + Raw AreaNorm Negative Surface Integral: 4.40333 across 43598.703125 (54.07%) mm^2 + +K +- (using 'lh.smoothwm'): 0.40466 +- 128.7805 mm^-2 + K Min: -137.69644 at vertex 119955 + K Max: 45999.28516 at vertex 35075 + K Curvature Calculation Type: discrete + K Mean Vertex Separation (Whole Surface): 0.85839 +- 0.14471 mm + K Total Surface Area: 80629.67188 mm^2 + K Total Number of Vertices: 127765 + K Average Vertex Area (Whole Surface): 0.63108 mm^2 + K Natural Surface Integral: 10.03039 + K Rectified Surface Integral: 3722.81152 + K Positive Surface Integral: 1866.42090 + K Negative Surface Integral: 1856.39050 + K Mean Natural Surface Integral: 0.00008 across 127765 (100.00%) vertices + K Mean Rectified Surface Integral: 0.02914 across 127765 (100.00%) vertices + K Mean Positive Surface Integral: 0.03180 across 58690 (45.94%) vertices + K Mean Negative Surface Integral: 0.02687 across 69075 (54.06%) vertices + K AreaNorm Natural Surface Integral: 0.00012 across 80629.421875 (100.00%) mm^2 + K AreaNorm Rectified Surface Integral: 0.04617 across 80629.421875 (100.00%) mm^2 + K AreaNorm Positive Surface Integral: 0.05603 across 33309.593750 (41.31%) mm^2 + K AreaNorm Negative Surface Integral: 0.03923 across 47319.820312 (58.69%) mm^2 + +H +- (using 'lh.smoothwm'): -0.02908 +- 3.3661 mm^-1 + H Min: -522.82898 at vertex 119812 + H Max: 1013.19629 at vertex 35075 + H Curvature Calculation Type: discrete + H Mean Vertex Separation (Whole Surface): 0.85839 +- 0.14471 mm + H Total Surface Area: 80629.67188 mm^2 + H Total Number of Vertices: 127765 + H Average Vertex Area (Whole Surface): 0.63108 mm^2 + H Natural Surface Integral: -1761.99780 + H Rectified Surface Integral: 13818.12891 + H Positive Surface Integral: 6028.06592 + H Negative Surface Integral: 7790.06348 + H Mean Natural Surface Integral: -0.01379 across 127765 (100.00%) vertices + H Mean Rectified Surface Integral: 0.10815 across 127765 (100.00%) vertices + H Mean Positive Surface Integral: 0.09073 across 66436 (52.00%) vertices + H Mean Negative Surface Integral: 0.12702 across 61329 (48.00%) vertices + H AreaNorm Natural Surface Integral: -0.02185 across 80629.421875 (100.00%) mm^2 + H AreaNorm Rectified Surface Integral: 0.17138 across 80629.421875 (100.00%) mm^2 + H AreaNorm Positive Surface Integral: 0.14318 across 42101.167969 (52.22%) mm^2 + H AreaNorm Negative Surface Integral: 0.20219 across 38528.816406 (47.78%) mm^2 + +k1 +- (using 'lh.smoothwm'): -0.06000 +- 6.6697 mm^-1 + k1 Min: -1045.17017 at vertex 119812 + k1 Max: 2003.43237 at vertex 35075 + k1 Curvature Calculation Type: discrete + k1 Mean Vertex Separation (Whole Surface): 0.85839 +- 0.14471 mm + k1 Total Surface Area: 80629.67188 mm^2 + k1 Total Number of Vertices: 127765 + k1 Average Vertex Area (Whole Surface): 0.63108 mm^2 + k1 Natural Surface Integral: -3943.13159 + k1 Rectified Surface Integral: 29239.86328 + k1 Positive Surface Integral: 12648.36621 + k1 Negative Surface Integral: 16591.49805 + k1 Mean Natural Surface Integral: -0.03086 across 127765 (100.00%) vertices + k1 Mean Rectified Surface Integral: 0.22886 across 127765 (100.00%) vertices + k1 Mean Positive Surface Integral: 0.19038 across 66436 (52.00%) vertices + k1 Mean Negative Surface Integral: 0.27053 across 61329 (48.00%) vertices + k1 AreaNorm Natural Surface Integral: -0.04890 across 80629.421875 (100.00%) mm^2 + k1 AreaNorm Rectified Surface Integral: 0.36265 across 80629.421875 (100.00%) mm^2 + k1 AreaNorm Positive Surface Integral: 0.30043 across 42101.167969 (52.22%) mm^2 + k1 AreaNorm Negative Surface Integral: 0.43063 across 38528.816406 (47.78%) mm^2 + +k2 +- (using 'lh.smoothwm'): 0.00183 +- 0.1699 mm^-1 + k2 Min: -14.41974 at vertex 67492 + k2 Max: 22.96024 at vertex 35075 + k2 Curvature Calculation Type: discrete + k2 Mean Vertex Separation (Whole Surface): 0.85839 +- 0.14471 mm + k2 Total Surface Area: 80629.67188 mm^2 + k2 Total Number of Vertices: 127765 + k2 Average Vertex Area (Whole Surface): 0.63108 mm^2 + k2 Natural Surface Integral: 419.13602 + k2 Rectified Surface Integral: 7187.33398 + k2 Positive Surface Integral: 3803.23486 + k2 Negative Surface Integral: 3384.09888 + k2 Mean Natural Surface Integral: 0.00328 across 127765 (100.00%) vertices + k2 Mean Rectified Surface Integral: 0.05625 across 127765 (100.00%) vertices + k2 Mean Positive Surface Integral: 0.05627 across 67591 (52.90%) vertices + k2 Mean Negative Surface Integral: 0.05624 across 60174 (47.10%) vertices + k2 AreaNorm Natural Surface Integral: 0.00520 across 80629.421875 (100.00%) mm^2 + k2 AreaNorm Rectified Surface Integral: 0.08914 across 80629.421875 (100.00%) mm^2 + k2 AreaNorm Positive Surface Integral: 0.08932 across 42580.980469 (52.81%) mm^2 + k2 AreaNorm Negative Surface Integral: 0.08894 across 38048.824219 (47.19%) mm^2 + +S +- (using 'lh.smoothwm'): 43.70791 +- 11439.3973 mm^-2 + S Min: 0.00000 at vertex 45 + S Max: 3922270.00000 at vertex 35075 + S Curvature Calculation Type: discrete + S Mean Vertex Separation (Whole Surface): 0.85839 +- 0.14471 mm + S Total Surface Area: 80629.67188 mm^2 + S Total Number of Vertices: 127765 + S Average Vertex Area (Whole Surface): 0.63108 mm^2 + S Natural Surface Integral: 22523.45703 + S Rectified Surface Integral: 22523.45703 + S Positive Surface Integral: 22523.45703 + S Negative Surface Integral: 0.00000 + S Mean Natural Surface Integral: 0.17629 across 127765 (100.00%) vertices + S Mean Rectified Surface Integral: 0.17629 across 127765 (100.00%) vertices + S Mean Positive Surface Integral: 0.17629 across 127765 (100.00%) vertices + S Mean Negative Surface Integral: 0.00000 across 0 (00.00%) vertices + S AreaNorm Natural Surface Integral: 0.27935 across 80629.421875 (100.00%) mm^2 + S AreaNorm Rectified Surface Integral: 0.27935 across 80629.421875 (100.00%) mm^2 + S AreaNorm Positive Surface Integral: 0.27935 across 80629.421875 (100.00%) mm^2 + S AreaNorm Negative Surface Integral: 0.00000 across 0.000000 (00.00%) mm^2 + +C +- (using 'lh.smoothwm'): 0.33225 +- 4.7062 mm^-2 + C Min: 0.00550 at vertex 75114 + C Max: 1416.73364 at vertex 35075 + C Curvature Calculation Type: discrete + C Mean Vertex Separation (Whole Surface): 0.85839 +- 0.14471 mm + C Total Surface Area: 80629.67188 mm^2 + C Total Number of Vertices: 127765 + C Average Vertex Area (Whole Surface): 0.63108 mm^2 + C Natural Surface Integral: 21689.17969 + C Rectified Surface Integral: 21689.17969 + C Positive Surface Integral: 21689.17969 + C Negative Surface Integral: 0.00000 + C Mean Natural Surface Integral: 0.16976 across 127765 (100.00%) vertices + C Mean Rectified Surface Integral: 0.16976 across 127765 (100.00%) vertices + C Mean Positive Surface Integral: 0.16976 across 127765 (100.00%) vertices + C Mean Negative Surface Integral: 0.00000 across 0 (00.00%) vertices + C AreaNorm Natural Surface Integral: 0.26900 across 80629.421875 (100.00%) mm^2 + C AreaNorm Rectified Surface Integral: 0.26900 across 80629.421875 (100.00%) mm^2 + C AreaNorm Positive Surface Integral: 0.26900 across 80629.421875 (100.00%) mm^2 + C AreaNorm Negative Surface Integral: 0.00000 across 0.000000 (00.00%) mm^2 + +BE +- (using 'lh.smoothwm'): 44.51705 +- 11687.2143 mm^-2 + BE Min: 0.00006 at vertex 75114 + BE Max: 4014268.50000 at vertex 35075 + BE Curvature Calculation Type: discrete + BE Mean Vertex Separation (Whole Surface): 0.85839 +- 0.14471 mm + BE Total Surface Area: 80629.67188 mm^2 + BE Total Number of Vertices: 127765 + BE Average Vertex Area (Whole Surface): 0.63108 mm^2 + BE Natural Surface Integral: 22542.37305 + BE Rectified Surface Integral: 22542.37305 + BE Positive Surface Integral: 22542.37305 + BE Negative Surface Integral: 0.00000 + BE Mean Natural Surface Integral: 0.17644 across 127765 (100.00%) vertices + BE Mean Rectified Surface Integral: 0.17644 across 127765 (100.00%) vertices + BE Mean Positive Surface Integral: 0.17644 across 127765 (100.00%) vertices + BE Mean Negative Surface Integral: 0.00000 across 0 (00.00%) vertices + BE AreaNorm Natural Surface Integral: 0.27958 across 80629.421875 (100.00%) mm^2 + BE AreaNorm Rectified Surface Integral: 0.27958 across 80629.421875 (100.00%) mm^2 + BE AreaNorm Positive Surface Integral: 0.27958 across 80629.421875 (100.00%) mm^2 + BE AreaNorm Negative Surface Integral: 0.00000 across 0.000000 (00.00%) mm^2 + +FI +- (using 'lh.smoothwm'): 44.03400 +- 11561.7650 mm^-2 + FI Min: 0.00000 at vertex 45 + FI Max: 3967742.00000 at vertex 35075 + FI Curvature Calculation Type: discrete + FI Mean Vertex Separation (Whole Surface): 0.85839 +- 0.14471 mm + FI Total Surface Area: 80629.67188 mm^2 + FI Total Number of Vertices: 127765 + FI Average Vertex Area (Whole Surface): 0.63108 mm^2 + FI Natural Surface Integral: 17500.04883 + FI Rectified Surface Integral: 17500.04883 + FI Positive Surface Integral: 17500.04883 + FI Negative Surface Integral: 0.00000 + FI Mean Natural Surface Integral: 0.13697 across 127765 (100.00%) vertices + FI Mean Rectified Surface Integral: 0.13697 across 127765 (100.00%) vertices + FI Mean Positive Surface Integral: 0.13697 across 127765 (100.00%) vertices + FI Mean Negative Surface Integral: 0.00000 across 0 (00.00%) vertices + FI AreaNorm Natural Surface Integral: 0.21704 across 80629.421875 (100.00%) mm^2 + FI AreaNorm Rectified Surface Integral: 0.21704 across 80629.421875 (100.00%) mm^2 + FI AreaNorm Positive Surface Integral: 0.21704 across 80629.421875 (100.00%) mm^2 + FI AreaNorm Negative Surface Integral: 0.00000 across 0.000000 (00.00%) mm^2 + +curv -- calculation type: discrete +curv -- Folding Index (FI): 1392.60962 +curv -- Intrinsic Curvature Index - positive (ICIp): 148.52505 +curv -- Intrinsic Curvature Index - negative (ICIn): 147.72687 +curv -- Intrinsic Curvature Index - natural (ICIt): 0.79819 + +Mean across 10 curvatures: 1.3289e+01 +- 2.0163e+01 + + diff --git a/tests/subjects/soichi/stats/lh.w-g.pct.stats b/tests/subjects/soichi/stats/lh.w-g.pct.stats new file mode 100644 index 0000000..b269bb2 --- /dev/null +++ b/tests/subjects/soichi/stats/lh.w-g.pct.stats @@ -0,0 +1,92 @@ +# Title Segmentation Statistics +# +# generating_program mri_segstats +# cvs_version 7.0.0 +# cmdline mri_segstats --in /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f/output/surf/lh.w-g.pct.mgh --annot output lh aparc --sum /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f/output/stats/lh.w-g.pct.stats --snr +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# anatomy_type surface +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# subjectname output +# Annot output lh aparc +# ColorTable /tmp/mri_segstats.tmp.output.lh.176.ctab +# ColorTableTimeStamp 2020/05/04 22:13:42 +# InVolFile /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f/output/surf/lh.w-g.pct.mgh +# InVolFileTimeStamp 2020/05/04 22:13:41 +# InVolFrame 0 +# Only reporting non-empty segmentations +# VertexArea_mm2 0.706017 +# TableCol 1 ColHeader Index +# TableCol 1 FieldName Index +# TableCol 1 Units NA +# TableCol 2 ColHeader SegId +# TableCol 2 FieldName Segmentation Id +# TableCol 2 Units NA +# TableCol 3 ColHeader NVertices +# TableCol 3 FieldName Number of Vertices +# TableCol 3 Units unitless +# TableCol 4 ColHeader Area_mm2 +# TableCol 4 FieldName Area +# TableCol 4 Units mm^2 +# TableCol 5 ColHeader StructName +# TableCol 5 FieldName Structure Name +# TableCol 5 Units NA +# TableCol 6 ColHeader Mean +# TableCol 6 FieldName Intensity Mean +# TableCol 6 Units unknown +# TableCol 7 ColHeader StdDev +# TableCol 7 FieldName Itensity StdDev +# TableCol 7 Units unknown +# TableCol 8 ColHeader Min +# TableCol 8 FieldName Intensity Min +# TableCol 8 Units unknown +# TableCol 9 ColHeader Max +# TableCol 9 FieldName Intensity Max +# TableCol 9 Units unknown +# TableCol 10 ColHeader Range +# TableCol 10 FieldName Intensity Range +# TableCol 10 Units unknown +# TableCol 11 ColHeader SNR +# TableCol 11 FieldName Intensity SNR +# TableCol 11 Units none +# NRows 35 +# NTableCols 11 +# ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range SNR + 1 1000 8797 5346.4 unknown 0.0000 0.0000 0.0000 0.0000 0.0000 -nan + 2 1001 1069 732.4 bankssts 32.2310 5.3339 13.6829 48.0815 34.3986 6.0427 + 3 1002 861 559.2 caudalanteriorcingulate 31.3112 4.6469 17.7241 46.0977 28.3735 6.7381 + 4 1003 3635 2504.1 caudalmiddlefrontal 29.5928 5.5888 10.0731 48.7656 38.6926 5.2950 + 5 1005 2419 1739.6 cuneus 25.2280 6.2290 3.6358 41.8373 38.2015 4.0501 + 6 1006 548 356.7 entorhinal 28.2899 7.3982 -7.7086 46.4734 54.1820 3.8239 + 7 1007 3637 2722.8 fusiform 28.7506 8.0572 -5.0947 52.6563 57.7510 3.5683 + 8 1008 5697 4169.8 inferiorparietal 30.2667 6.5324 2.9106 55.0659 52.1553 4.6333 + 9 1009 3670 2730.3 inferiortemporal 29.4551 7.6850 -1.7111 56.8518 58.5629 3.8328 + 10 1010 1534 1043.5 isthmuscingulate 26.1780 7.1462 -0.3036 44.9696 45.2732 3.6632 + 11 1011 7117 5175.7 lateraloccipital 26.3339 7.2197 -7.5046 59.8515 67.3560 3.6475 + 12 1012 3716 2627.1 lateralorbitofrontal 30.7968 8.8976 -2.6993 59.8120 62.5113 3.4612 + 13 1013 4256 3297.0 lingual 24.2993 8.0033 -25.3325 45.9461 71.2786 3.0361 + 14 1014 2868 1978.5 medialorbitofrontal 27.3374 12.8968 -58.0681 61.0749 119.1430 2.1197 + 15 1015 3466 2711.5 middletemporal 27.2499 7.7445 -27.7069 55.6032 83.3101 3.5186 + 16 1016 869 556.6 parahippocampal 30.6419 6.8118 9.0265 49.0164 39.9899 4.4983 + 17 1017 2463 1524.7 paracentral 26.1351 7.9326 3.9247 51.3411 47.4164 3.2946 + 18 1018 2485 1775.3 parsopercularis 31.0387 6.1284 8.3338 51.9747 43.6409 5.0647 + 19 1019 890 703.9 parsorbitalis 29.9108 7.2716 1.1074 53.7103 52.6029 4.1134 + 20 1020 1980 1437.7 parstriangularis 30.2547 7.0696 5.0913 57.3916 52.3003 4.2795 + 21 1021 2096 1523.6 pericalcarine 23.4158 5.6427 2.5075 46.6393 44.1318 4.1497 + 22 1022 6436 4474.9 postcentral 26.7588 6.7065 -7.2445 52.7955 60.0399 3.9900 + 23 1023 1883 1261.1 posteriorcingulate 29.2603 7.3855 -1.1920 50.3276 51.5196 3.9618 + 24 1024 8010 5323.7 precentral 24.3475 7.2082 1.0214 47.3662 46.3448 3.3777 + 25 1025 4973 3519.0 precuneus 29.6542 6.4972 -12.0707 49.6958 61.7665 4.5641 + 26 1026 1336 981.4 rostralanteriorcingulate 31.3890 11.7888 -33.9684 70.7572 104.7256 2.6626 + 27 1027 7137 5404.1 rostralmiddlefrontal 29.2840 7.3864 -6.2795 64.3289 70.6084 3.9646 + 28 1028 11318 7858.0 superiorfrontal 30.6001 6.6785 6.2469 55.9067 49.6598 4.5819 + 29 1029 6602 4641.6 superiorparietal 28.5048 6.1060 -17.2151 49.2834 66.4985 4.6684 + 30 1030 5500 3856.9 superiortemporal 30.7228 7.6514 -42.4546 68.2752 110.7298 4.0153 + 31 1031 5498 4140.2 supramarginal 29.1747 7.1918 -10.4217 53.5430 63.9648 4.0567 + 32 1032 310 264.3 frontalpole 29.4264 11.7401 -3.3167 54.0117 57.3284 2.5065 + 33 1033 717 540.0 temporalpole 29.7048 9.6077 -1.6414 55.7050 57.3464 3.0918 + 34 1034 757 535.3 transversetemporal 24.5779 6.8058 -4.0446 44.1972 48.2418 3.6113 + 35 1035 3215 2187.4 insula 27.3214 8.4217 0.9642 57.2715 56.3072 3.2442 diff --git a/tests/subjects/soichi/stats/rh.BA_exvivo.stats b/tests/subjects/soichi/stats/rh.BA_exvivo.stats new file mode 100644 index 0000000..4f79178 --- /dev/null +++ b/tests/subjects/soichi/stats/rh.BA_exvivo.stats @@ -0,0 +1,74 @@ +# Table of FreeSurfer cortical parcellation anatomical statistics +# +# CreationTime 2020/05/04-22:23:59-GMT +# generating_program mris_anatomical_stats +# cvs_version 7.0.0 +# mrisurf.c-cvs_version 7.0.0 +# cmdline mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab output rh white +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# anatomy_type surface +# subjectname output +# hemi rh +# AnnotationFile ./rh.BA_exvivo.annot +# AnnotationFileTimeStamp 2020/05/04 22:23:55 +# Measure Cortex, NumVert, Number of Vertices, 124680, unitless +# Measure Cortex, WhiteSurfArea, White Surface Total Area, 88998.7, mm^2 +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000, mm^3 +# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1157593.000000, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696158, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000, mm^3 +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# NTableCols 10 +# TableCol 1 ColHeader StructName +# TableCol 1 FieldName Structure Name +# TableCol 1 Units NA +# TableCol 2 ColHeader NumVert +# TableCol 2 FieldName Number of Vertices +# TableCol 2 Units unitless +# TableCol 3 ColHeader SurfArea +# TableCol 3 FieldName Surface Area +# TableCol 3 Units mm^2 +# TableCol 4 ColHeader GrayVol +# TableCol 4 FieldName Gray Matter Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader ThickAvg +# TableCol 5 FieldName Average Thickness +# TableCol 5 Units mm +# TableCol 6 ColHeader ThickStd +# TableCol 6 FieldName Thickness StdDev +# TableCol 6 Units mm +# TableCol 7 ColHeader MeanCurv +# TableCol 7 FieldName Integrated Rectified Mean Curvature +# TableCol 7 Units mm^-1 +# TableCol 8 ColHeader GausCurv +# TableCol 8 FieldName Integrated Rectified Gaussian Curvature +# TableCol 8 Units mm^-2 +# TableCol 9 ColHeader FoldInd +# TableCol 9 FieldName Folding Index +# TableCol 9 Units unitless +# TableCol 10 ColHeader CurvInd +# TableCol 10 FieldName Intrinsic Curvature Index +# TableCol 10 Units unitless +# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd +BA1_exvivo 930 649 1737 2.100 0.480 0.155 0.039 13 1.7 +BA2_exvivo 3134 2104 4086 1.917 0.451 0.103 0.021 20 2.5 +BA3a_exvivo 1089 718 1008 1.853 0.435 0.128 0.028 10 1.2 +BA3b_exvivo 1794 1267 2578 1.751 0.531 0.104 0.021 12 1.7 +BA4a_exvivo 1520 881 2971 2.877 0.672 0.100 0.028 9 1.9 +BA4p_exvivo 1249 801 1810 2.269 0.570 0.091 0.019 6 0.9 +BA6_exvivo 8152 5352 17057 2.813 0.621 0.114 0.024 64 8.3 +BA44_exvivo 3838 2774 7530 2.500 0.565 0.124 0.027 36 4.4 +BA45_exvivo 3951 3075 9056 2.442 0.662 0.141 0.037 48 6.2 +V1_exvivo 3891 2885 5389 1.792 0.531 0.150 0.040 47 6.7 +V2_exvivo 7820 5770 12321 2.037 0.535 0.156 0.042 106 14.0 +MT_exvivo 1835 1377 3357 2.205 0.505 0.149 0.037 21 2.9 +perirhinal_exvivo 287 210 709 2.758 0.562 0.100 0.023 1 0.4 +entorhinal_exvivo 462 320 1567 2.977 1.227 0.123 0.033 5 0.5 diff --git a/tests/subjects/soichi/stats/rh.BA_exvivo.thresh.stats b/tests/subjects/soichi/stats/rh.BA_exvivo.thresh.stats new file mode 100644 index 0000000..a7e3705 --- /dev/null +++ b/tests/subjects/soichi/stats/rh.BA_exvivo.thresh.stats @@ -0,0 +1,74 @@ +# Table of FreeSurfer cortical parcellation anatomical statistics +# +# CreationTime 2020/05/04-22:24:03-GMT +# generating_program mris_anatomical_stats +# cvs_version 7.0.0 +# mrisurf.c-cvs_version 7.0.0 +# cmdline mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab output rh white +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# anatomy_type surface +# subjectname output +# hemi rh +# AnnotationFile ./rh.BA_exvivo.thresh.annot +# AnnotationFileTimeStamp 2020/05/04 22:23:56 +# Measure Cortex, NumVert, Number of Vertices, 124680, unitless +# Measure Cortex, WhiteSurfArea, White Surface Total Area, 88998.7, mm^2 +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000, mm^3 +# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1157593.000000, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696158, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000, mm^3 +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# NTableCols 10 +# TableCol 1 ColHeader StructName +# TableCol 1 FieldName Structure Name +# TableCol 1 Units NA +# TableCol 2 ColHeader NumVert +# TableCol 2 FieldName Number of Vertices +# TableCol 2 Units unitless +# TableCol 3 ColHeader SurfArea +# TableCol 3 FieldName Surface Area +# TableCol 3 Units mm^2 +# TableCol 4 ColHeader GrayVol +# TableCol 4 FieldName Gray Matter Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader ThickAvg +# TableCol 5 FieldName Average Thickness +# TableCol 5 Units mm +# TableCol 6 ColHeader ThickStd +# TableCol 6 FieldName Thickness StdDev +# TableCol 6 Units mm +# TableCol 7 ColHeader MeanCurv +# TableCol 7 FieldName Integrated Rectified Mean Curvature +# TableCol 7 Units mm^-1 +# TableCol 8 ColHeader GausCurv +# TableCol 8 FieldName Integrated Rectified Gaussian Curvature +# TableCol 8 Units mm^-2 +# TableCol 9 ColHeader FoldInd +# TableCol 9 FieldName Folding Index +# TableCol 9 Units unitless +# TableCol 10 ColHeader CurvInd +# TableCol 10 FieldName Intrinsic Curvature Index +# TableCol 10 Units unitless +# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd +BA1_exvivo 634 455 1215 2.084 0.461 0.162 0.042 8 1.3 +BA2_exvivo 1783 1203 2516 1.911 0.460 0.093 0.016 9 1.2 +BA3a_exvivo 982 642 826 1.852 0.411 0.135 0.027 9 1.2 +BA3b_exvivo 1404 962 1561 1.574 0.361 0.086 0.015 6 0.9 +BA4a_exvivo 967 527 1977 3.050 0.631 0.108 0.036 7 1.5 +BA4p_exvivo 1049 672 1437 2.180 0.562 0.092 0.021 4 0.9 +BA6_exvivo 5250 3410 10858 2.791 0.604 0.114 0.025 42 5.4 +BA44_exvivo 969 718 2031 2.316 0.535 0.135 0.024 12 0.9 +BA45_exvivo 893 755 2738 2.690 0.781 0.156 0.050 14 1.9 +V1_exvivo 3749 2739 4991 1.778 0.520 0.147 0.040 44 6.2 +V2_exvivo 4117 3119 6544 1.982 0.556 0.161 0.046 58 8.0 +MT_exvivo 245 182 395 2.050 0.414 0.148 0.049 3 0.4 +perirhinal_exvivo 24 17 54 2.892 0.427 0.055 0.014 0 0.0 +entorhinal_exvivo 451 296 1500 3.200 0.820 0.095 0.024 3 0.3 diff --git a/tests/subjects/soichi/stats/rh.aparc.DKTatlas.stats b/tests/subjects/soichi/stats/rh.aparc.DKTatlas.stats new file mode 100644 index 0000000..c08f762 --- /dev/null +++ b/tests/subjects/soichi/stats/rh.aparc.DKTatlas.stats @@ -0,0 +1,92 @@ +# Table of FreeSurfer cortical parcellation anatomical statistics +# +# CreationTime 2020/05/04-22:20:53-GMT +# generating_program mris_anatomical_stats +# cvs_version 7.0.0 +# mrisurf.c-cvs_version 7.0.0 +# cmdline mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab output rh white +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# anatomy_type surface +# subjectname output +# hemi rh +# AnnotationFile ../label/rh.aparc.DKTatlas.annot +# AnnotationFileTimeStamp 2020/05/04 22:13:39 +# Measure Cortex, NumVert, Number of Vertices, 115827, unitless +# Measure Cortex, WhiteSurfArea, White Surface Total Area, 83579.2, mm^2 +# Measure Cortex, MeanThickness, Mean Thickness, 2.35815, mm +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000, mm^3 +# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1157593.000000, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696158, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000, mm^3 +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# NTableCols 10 +# TableCol 1 ColHeader StructName +# TableCol 1 FieldName Structure Name +# TableCol 1 Units NA +# TableCol 2 ColHeader NumVert +# TableCol 2 FieldName Number of Vertices +# TableCol 2 Units unitless +# TableCol 3 ColHeader SurfArea +# TableCol 3 FieldName Surface Area +# TableCol 3 Units mm^2 +# TableCol 4 ColHeader GrayVol +# TableCol 4 FieldName Gray Matter Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader ThickAvg +# TableCol 5 FieldName Average Thickness +# TableCol 5 Units mm +# TableCol 6 ColHeader ThickStd +# TableCol 6 FieldName Thickness StdDev +# TableCol 6 Units mm +# TableCol 7 ColHeader MeanCurv +# TableCol 7 FieldName Integrated Rectified Mean Curvature +# TableCol 7 Units mm^-1 +# TableCol 8 ColHeader GausCurv +# TableCol 8 FieldName Integrated Rectified Gaussian Curvature +# TableCol 8 Units mm^-2 +# TableCol 9 ColHeader FoldInd +# TableCol 9 FieldName Folding Index +# TableCol 9 Units unitless +# TableCol 10 ColHeader CurvInd +# TableCol 10 FieldName Intrinsic Curvature Index +# TableCol 10 Units unitless +# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd +caudalanteriorcingulate 1234 843 2483 2.826 0.653 0.116 0.021 12 1.1 +caudalmiddlefrontal 3263 2302 6175 2.437 0.598 0.121 0.024 28 3.3 +cuneus 3039 2191 4262 1.875 0.433 0.143 0.034 34 4.3 +entorhinal 339 221 1184 3.262 0.690 0.082 0.020 2 0.2 +fusiform 3025 2175 5785 2.301 0.632 0.134 0.032 33 4.3 +inferiorparietal 7091 5312 13161 2.156 0.571 0.134 0.030 83 9.3 +inferiortemporal 3125 2424 7370 2.404 0.740 0.150 0.040 43 5.6 +isthmuscingulate 1429 1072 2726 2.337 0.645 0.157 0.047 24 2.8 +lateraloccipital 6301 4719 10910 2.156 0.570 0.159 0.041 85 10.7 +lateralorbitofrontal 4093 3005 8648 2.499 0.811 0.157 0.049 75 8.5 +lingual 4818 3551 8027 2.104 0.597 0.146 0.040 62 8.4 +medialorbitofrontal 2435 1814 5921 2.650 0.902 0.138 0.043 37 4.7 +middletemporal 4283 3366 9002 2.240 0.636 0.133 0.034 54 6.3 +parahippocampal 940 605 1737 2.401 0.753 0.094 0.020 6 0.7 +paracentral 2462 1485 4530 2.772 0.712 0.097 0.023 15 2.3 +parsopercularis 2317 1693 4539 2.421 0.664 0.127 0.028 24 2.9 +parsorbitalis 1029 772 2232 2.399 0.653 0.128 0.028 11 1.1 +parstriangularis 2131 1625 4888 2.521 0.651 0.138 0.039 24 3.5 +pericalcarine 2216 1566 2263 1.639 0.413 0.143 0.037 24 3.3 +postcentral 6477 4492 9747 1.963 0.553 0.115 0.025 53 6.8 +posteriorcingulate 1839 1312 3870 2.648 0.790 0.137 0.030 23 2.3 +precentral 7455 4896 12964 2.454 0.576 0.117 0.026 58 8.7 +precuneus 5795 4018 10401 2.417 0.594 0.123 0.026 53 6.1 +rostralanteriorcingulate 1162 887 2740 2.556 0.842 0.146 0.038 15 2.1 +rostralmiddlefrontal 5319 4203 11722 2.318 0.704 0.146 0.038 68 9.0 +superiorfrontal 11609 8131 27456 2.845 0.717 0.125 0.031 105 14.5 +superiorparietal 6308 4392 9679 2.032 0.542 0.122 0.024 57 6.1 +superiortemporal 6551 4880 13659 2.356 0.710 0.131 0.037 86 10.9 +supramarginal 4425 3332 8213 2.237 0.625 0.139 0.036 54 7.0 +transversetemporal 522 410 954 2.026 0.540 0.192 0.069 14 1.4 +insula 2795 1885 5518 2.942 0.772 0.110 0.024 21 2.7 diff --git a/tests/subjects/soichi/stats/rh.aparc.a2009s.stats b/tests/subjects/soichi/stats/rh.aparc.a2009s.stats new file mode 100644 index 0000000..d96402a --- /dev/null +++ b/tests/subjects/soichi/stats/rh.aparc.a2009s.stats @@ -0,0 +1,135 @@ +# Table of FreeSurfer cortical parcellation anatomical statistics +# +# CreationTime 2020/05/04-22:20:40-GMT +# generating_program mris_anatomical_stats +# cvs_version 7.0.0 +# mrisurf.c-cvs_version 7.0.0 +# cmdline mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab output rh white +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# anatomy_type surface +# subjectname output +# hemi rh +# AnnotationFile ../label/rh.aparc.a2009s.annot +# AnnotationFileTimeStamp 2020/05/04 22:13:27 +# Measure Cortex, NumVert, Number of Vertices, 115827, unitless +# Measure Cortex, WhiteSurfArea, White Surface Total Area, 83579.2, mm^2 +# Measure Cortex, MeanThickness, Mean Thickness, 2.35815, mm +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000, mm^3 +# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1157593.000000, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696158, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000, mm^3 +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# NTableCols 10 +# TableCol 1 ColHeader StructName +# TableCol 1 FieldName Structure Name +# TableCol 1 Units NA +# TableCol 2 ColHeader NumVert +# TableCol 2 FieldName Number of Vertices +# TableCol 2 Units unitless +# TableCol 3 ColHeader SurfArea +# TableCol 3 FieldName Surface Area +# TableCol 3 Units mm^2 +# TableCol 4 ColHeader GrayVol +# TableCol 4 FieldName Gray Matter Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader ThickAvg +# TableCol 5 FieldName Average Thickness +# TableCol 5 Units mm +# TableCol 6 ColHeader ThickStd +# TableCol 6 FieldName Thickness StdDev +# TableCol 6 Units mm +# TableCol 7 ColHeader MeanCurv +# TableCol 7 FieldName Integrated Rectified Mean Curvature +# TableCol 7 Units mm^-1 +# TableCol 8 ColHeader GausCurv +# TableCol 8 FieldName Integrated Rectified Gaussian Curvature +# TableCol 8 Units mm^-2 +# TableCol 9 ColHeader FoldInd +# TableCol 9 FieldName Folding Index +# TableCol 9 Units unitless +# TableCol 10 ColHeader CurvInd +# TableCol 10 FieldName Intrinsic Curvature Index +# TableCol 10 Units unitless +# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd +G_and_S_frontomargin 629 550 2032 2.720 0.788 0.166 0.052 10 1.2 +G_and_S_occipital_inf 975 763 2163 2.444 0.589 0.147 0.038 11 1.6 +G_and_S_paracentral 1394 835 2680 2.611 0.745 0.105 0.027 10 1.6 +G_and_S_subcentral 1536 1152 3299 2.443 0.554 0.140 0.036 18 2.2 +G_and_S_transv_frontopol 907 800 3069 2.782 0.672 0.193 0.063 18 2.5 +G_and_S_cingul-Ant 2731 1859 6291 2.725 0.893 0.112 0.028 23 3.2 +G_and_S_cingul-Mid-Ant 1359 929 2537 2.656 0.499 0.102 0.019 10 1.1 +G_and_S_cingul-Mid-Post 1384 950 2911 2.832 0.695 0.109 0.025 11 1.5 +G_cingul-Post-dorsal 662 483 1901 3.144 0.686 0.161 0.042 10 1.3 +G_cingul-Post-ventral 338 253 730 2.246 0.712 0.181 0.073 9 1.2 +G_cuneus 2360 1719 3295 1.787 0.385 0.154 0.039 30 3.8 +G_front_inf-Opercular 1288 1002 3363 2.629 0.623 0.145 0.036 19 2.0 +G_front_inf-Orbital 548 444 1617 2.530 0.595 0.175 0.058 9 1.3 +G_front_inf-Triangul 771 670 2513 2.796 0.701 0.164 0.053 13 1.8 +G_front_middle 3623 2949 9520 2.452 0.717 0.160 0.042 58 6.9 +G_front_sup 6327 4406 17517 3.122 0.624 0.136 0.034 67 9.0 +G_Ins_lg_and_S_cent_ins 714 477 1398 2.746 1.082 0.146 0.052 12 1.6 +G_insular_short 595 401 1739 3.161 1.031 0.130 0.047 8 1.1 +G_occipital_middle 2030 1581 4875 2.546 0.608 0.167 0.043 34 3.8 +G_occipital_sup 1466 1057 2700 2.140 0.524 0.144 0.032 17 2.1 +G_oc-temp_lat-fusifor 1279 953 3135 2.478 0.552 0.147 0.038 17 2.2 +G_oc-temp_med-Lingual 2940 2228 5472 2.122 0.648 0.159 0.045 43 5.9 +G_oc-temp_med-Parahip 821 524 2280 2.927 0.780 0.103 0.029 7 0.7 +G_orbital 2675 2119 6867 2.502 0.847 0.177 0.059 63 7.1 +G_pariet_inf-Angular 2301 1811 4843 2.130 0.585 0.148 0.034 31 3.3 +G_pariet_inf-Supramar 2075 1709 4618 2.202 0.652 0.165 0.050 37 4.5 +G_parietal_sup 2717 1947 4965 2.067 0.610 0.134 0.026 28 3.0 +G_postcentral 2073 1497 3549 1.916 0.506 0.131 0.031 21 2.8 +G_precentral 2797 1781 6049 2.649 0.595 0.123 0.032 25 4.0 +G_precuneus 2313 1694 5233 2.406 0.672 0.143 0.032 29 3.2 +G_rectus 948 760 2740 2.630 0.712 0.155 0.044 21 1.8 +G_subcallosal 685 535 979 2.077 0.700 0.185 0.072 12 2.1 +G_temp_sup-G_T_transv 603 467 1222 2.197 0.633 0.201 0.072 16 1.7 +G_temp_sup-Lateral 1781 1529 4792 2.337 0.686 0.161 0.052 36 4.4 +G_temp_sup-Plan_polar 802 581 1895 2.726 0.885 0.127 0.040 11 1.5 +G_temp_sup-Plan_tempo 578 403 1007 2.117 0.629 0.082 0.013 2 0.3 +G_temporal_inf 1580 1279 4413 2.583 0.769 0.163 0.049 26 3.4 +G_temporal_middle 1976 1710 5103 2.266 0.681 0.154 0.045 34 3.9 +Lat_Fis-ant-Horizont 319 217 386 1.988 0.557 0.105 0.016 2 0.2 +Lat_Fis-ant-Vertical 177 129 213 1.875 0.358 0.124 0.018 1 0.2 +Lat_Fis-post 1227 817 1648 2.563 0.494 0.117 0.025 9 1.2 +Pole_occipital 3047 2381 5167 1.959 0.578 0.168 0.049 47 6.1 +Pole_temporal 1440 1201 4468 2.576 0.793 0.151 0.039 20 2.7 +S_calcarine 2581 1785 2885 1.866 0.508 0.127 0.031 24 3.4 +S_central 2964 1946 3125 1.884 0.509 0.100 0.019 16 2.3 +S_cingul-Marginalis 1226 813 1665 2.153 0.464 0.094 0.016 6 0.8 +S_circular_insula_ant 660 430 858 2.313 0.536 0.092 0.016 3 0.4 +S_circular_insula_inf 1152 748 1588 2.442 0.598 0.087 0.016 5 0.8 +S_circular_insula_sup 1511 979 2335 2.805 0.582 0.095 0.017 6 1.1 +S_collat_transv_ant 851 583 1368 2.173 0.754 0.117 0.021 7 0.8 +S_collat_transv_post 483 348 522 1.976 0.330 0.177 0.045 7 1.0 +S_front_inf 2322 1663 3565 2.237 0.503 0.122 0.027 19 2.7 +S_front_middle 1753 1214 2706 2.160 0.713 0.110 0.025 11 1.6 +S_front_sup 2220 1502 3444 2.387 0.575 0.097 0.018 11 1.7 +S_interm_prim-Jensen 397 267 468 1.748 0.455 0.092 0.018 2 0.3 +S_intrapariet_and_P_trans 3081 2116 3751 1.948 0.427 0.119 0.023 27 2.9 +S_oc_middle_and_Lunatus 782 526 1052 2.154 0.493 0.129 0.027 7 0.8 +S_oc_sup_and_transversal 1313 891 1634 1.980 0.471 0.120 0.025 11 1.4 +S_occipital_ant 669 492 999 1.938 0.378 0.141 0.037 7 0.9 +S_oc-temp_lat 711 525 1197 2.072 0.609 0.145 0.037 8 1.2 +S_oc-temp_med_and_Lingual 2057 1356 2710 2.162 0.549 0.101 0.019 11 1.6 +S_orbital_lateral 432 311 646 2.495 0.537 0.117 0.022 2 0.4 +S_orbital_med-olfact 800 521 983 2.194 0.641 0.101 0.017 5 0.5 +S_orbital-H_Shaped 1225 847 2242 2.643 0.661 0.121 0.028 11 1.3 +S_parieto_occipital 2522 1683 3592 2.339 0.553 0.113 0.020 18 2.2 +S_pericallosal 1418 958 1775 2.447 0.776 0.139 0.024 18 1.2 +S_postcentral 2559 1646 2879 1.974 0.442 0.098 0.016 14 1.8 +S_precentral-inf-part 2059 1380 3182 2.512 0.517 0.111 0.020 13 1.7 +S_precentral-sup-part 1436 926 1955 2.391 0.480 0.100 0.020 8 1.2 +S_suborbital 317 207 701 3.280 0.981 0.089 0.011 1 0.2 +S_subparietal 1160 797 1867 2.508 0.601 0.110 0.024 8 1.0 +S_temporal_inf 524 383 772 1.917 0.532 0.125 0.029 4 0.6 +S_temporal_sup 5607 4002 8766 2.175 0.556 0.117 0.025 51 5.8 +S_temporal_transverse 244 180 338 2.240 0.270 0.135 0.019 2 0.2 diff --git a/tests/subjects/soichi/stats/rh.aparc.pial.stats b/tests/subjects/soichi/stats/rh.aparc.pial.stats new file mode 100644 index 0000000..2ef9303 --- /dev/null +++ b/tests/subjects/soichi/stats/rh.aparc.pial.stats @@ -0,0 +1,95 @@ +# Table of FreeSurfer cortical parcellation anatomical statistics +# +# CreationTime 2020/05/04-22:20:27-GMT +# generating_program mris_anatomical_stats +# cvs_version 7.0.0 +# mrisurf.c-cvs_version 7.0.0 +# cmdline mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab output rh pial +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# anatomy_type surface +# subjectname output +# hemi rh +# AnnotationFile ../label/rh.aparc.annot +# AnnotationFileTimeStamp 2020/05/04 21:58:13 +# Measure Cortex, NumVert, Number of Vertices, 115827, unitless +# Measure Cortex, PialSurfArea, Pial Surface Total Area, 106685, mm^2 +# Measure Cortex, MeanThickness, Mean Thickness, 2.35815, mm +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000, mm^3 +# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1157593.000000, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696158, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000, mm^3 +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# NTableCols 10 +# TableCol 1 ColHeader StructName +# TableCol 1 FieldName Structure Name +# TableCol 1 Units NA +# TableCol 2 ColHeader NumVert +# TableCol 2 FieldName Number of Vertices +# TableCol 2 Units unitless +# TableCol 3 ColHeader SurfArea +# TableCol 3 FieldName Surface Area +# TableCol 3 Units mm^2 +# TableCol 4 ColHeader GrayVol +# TableCol 4 FieldName Gray Matter Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader ThickAvg +# TableCol 5 FieldName Average Thickness +# TableCol 5 Units mm +# TableCol 6 ColHeader ThickStd +# TableCol 6 FieldName Thickness StdDev +# TableCol 6 Units mm +# TableCol 7 ColHeader MeanCurv +# TableCol 7 FieldName Integrated Rectified Mean Curvature +# TableCol 7 Units mm^-1 +# TableCol 8 ColHeader GausCurv +# TableCol 8 FieldName Integrated Rectified Gaussian Curvature +# TableCol 8 Units mm^-2 +# TableCol 9 ColHeader FoldInd +# TableCol 9 FieldName Folding Index +# TableCol 9 Units unitless +# TableCol 10 ColHeader CurvInd +# TableCol 10 FieldName Intrinsic Curvature Index +# TableCol 10 Units unitless +# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd +bankssts 1094 826 1725 2.215 0.544 0.136 0.034 17 1.5 +caudalanteriorcingulate 1137 938 2327 2.842 0.667 0.188 0.051 65 2.2 +caudalmiddlefrontal 3126 2625 5978 2.447 0.605 0.142 0.034 40 4.4 +cuneus 2446 2141 3537 1.886 0.407 0.156 0.041 37 4.2 +entorhinal 448 689 1599 3.171 0.707 0.291 0.075 9 1.9 +fusiform 3194 3044 6223 2.315 0.635 0.176 0.049 81 6.5 +inferiorparietal 7290 7098 13619 2.161 0.568 0.170 0.038 136 12.1 +inferiortemporal 2872 3289 6636 2.380 0.757 0.205 0.050 56 6.3 +isthmuscingulate 1455 1356 2785 2.351 0.673 0.195 0.074 131 4.6 +lateraloccipital 6205 5533 10849 2.162 0.568 0.171 0.048 375 11.1 +lateralorbitofrontal 3755 3379 7526 2.476 0.734 0.181 0.050 135 8.3 +lingual 4863 4381 8074 2.098 0.596 0.161 0.045 101 8.8 +medialorbitofrontal 3103 3228 7261 2.644 0.956 0.192 0.074 109 6.9 +middletemporal 3518 4471 7625 2.212 0.647 0.206 0.046 61 7.3 +parahippocampal 888 870 1675 2.425 0.763 0.223 0.070 19 3.0 +paracentral 2315 1629 4190 2.762 0.727 0.105 0.024 24 2.3 +parsopercularis 2127 1923 4214 2.456 0.669 0.177 0.054 54 4.8 +parsorbitalis 1076 1159 2404 2.526 0.734 0.182 0.045 22 1.7 +parstriangularis 2087 2311 4946 2.468 0.676 0.189 0.042 35 3.9 +pericalcarine 2258 1401 2304 1.634 0.414 0.120 0.036 52 2.8 +postcentral 5861 5150 8849 1.960 0.561 0.142 0.032 83 8.1 +posteriorcingulate 1769 1548 3777 2.662 0.781 0.190 0.058 132 3.7 +precentral 7650 5694 13170 2.460 0.581 0.122 0.031 126 9.9 +precuneus 5751 4425 10004 2.406 0.595 0.143 0.037 142 8.7 +rostralanteriorcingulate 827 1085 2414 2.889 0.686 0.212 0.045 16 2.0 +rostralmiddlefrontal 7032 7493 15442 2.365 0.687 0.193 0.046 152 14.1 +superiorfrontal 9449 8503 22074 2.877 0.688 0.154 0.039 178 14.9 +superiorparietal 7647 6387 11973 2.044 0.551 0.140 0.033 110 9.8 +superiortemporal 5052 5097 10104 2.320 0.650 0.198 0.055 124 12.4 +supramarginal 4621 4386 8461 2.207 0.616 0.176 0.046 101 8.2 +frontalpole 372 623 1574 3.211 0.790 0.258 0.052 7 0.9 +temporalpole 582 906 2030 3.120 0.834 0.295 0.080 17 2.1 +transversetemporal 538 608 998 2.060 0.552 0.236 0.062 22 1.4 +insula 3419 2492 6398 2.765 0.876 0.188 0.062 96 10.0 diff --git a/tests/subjects/soichi/stats/rh.aparc.stats b/tests/subjects/soichi/stats/rh.aparc.stats new file mode 100644 index 0000000..254b276 --- /dev/null +++ b/tests/subjects/soichi/stats/rh.aparc.stats @@ -0,0 +1,95 @@ +# Table of FreeSurfer cortical parcellation anatomical statistics +# +# CreationTime 2020/05/04-22:20:26-GMT +# generating_program mris_anatomical_stats +# cvs_version 7.0.0 +# mrisurf.c-cvs_version 7.0.0 +# cmdline mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab output rh white +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# anatomy_type surface +# subjectname output +# hemi rh +# AnnotationFile ../label/rh.aparc.annot +# AnnotationFileTimeStamp 2020/05/04 21:58:13 +# Measure Cortex, NumVert, Number of Vertices, 115827, unitless +# Measure Cortex, WhiteSurfArea, White Surface Total Area, 83579.2, mm^2 +# Measure Cortex, MeanThickness, Mean Thickness, 2.35815, mm +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1169408.000000, mm^3 +# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1157593.000000, mm^3 +# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1157593.000000, mm^3 +# Measure Cortex, CortexVol, Total cortical gray matter volume, 454587.696158, mm^3 +# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1023873.000000, mm^3 +# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1012058.000000, mm^3 +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# NTableCols 10 +# TableCol 1 ColHeader StructName +# TableCol 1 FieldName Structure Name +# TableCol 1 Units NA +# TableCol 2 ColHeader NumVert +# TableCol 2 FieldName Number of Vertices +# TableCol 2 Units unitless +# TableCol 3 ColHeader SurfArea +# TableCol 3 FieldName Surface Area +# TableCol 3 Units mm^2 +# TableCol 4 ColHeader GrayVol +# TableCol 4 FieldName Gray Matter Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader ThickAvg +# TableCol 5 FieldName Average Thickness +# TableCol 5 Units mm +# TableCol 6 ColHeader ThickStd +# TableCol 6 FieldName Thickness StdDev +# TableCol 6 Units mm +# TableCol 7 ColHeader MeanCurv +# TableCol 7 FieldName Integrated Rectified Mean Curvature +# TableCol 7 Units mm^-1 +# TableCol 8 ColHeader GausCurv +# TableCol 8 FieldName Integrated Rectified Gaussian Curvature +# TableCol 8 Units mm^-2 +# TableCol 9 ColHeader FoldInd +# TableCol 9 FieldName Folding Index +# TableCol 9 Units unitless +# TableCol 10 ColHeader CurvInd +# TableCol 10 FieldName Intrinsic Curvature Index +# TableCol 10 Units unitless +# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd +bankssts 1094 757 1725 2.215 0.544 0.109 0.025 9 1.1 +caudalanteriorcingulate 1137 780 2327 2.842 0.667 0.116 0.021 11 1.0 +caudalmiddlefrontal 3126 2218 5978 2.447 0.605 0.122 0.024 28 3.1 +cuneus 2446 1781 3537 1.886 0.407 0.151 0.038 30 4.0 +entorhinal 448 310 1599 3.171 0.707 0.103 0.028 3 0.5 +fusiform 3194 2330 6223 2.315 0.635 0.134 0.032 36 4.5 +inferiorparietal 7290 5467 13619 2.161 0.568 0.135 0.030 86 9.4 +inferiortemporal 2872 2203 6636 2.380 0.757 0.148 0.040 39 4.9 +isthmuscingulate 1455 1085 2785 2.351 0.673 0.157 0.046 24 2.8 +lateraloccipital 6205 4673 10849 2.162 0.568 0.160 0.042 84 10.6 +lateralorbitofrontal 3755 2748 7526 2.476 0.734 0.144 0.042 58 6.7 +lingual 4863 3579 8074 2.098 0.596 0.146 0.040 63 8.5 +medialorbitofrontal 3103 2244 7261 2.644 0.956 0.130 0.035 39 4.5 +middletemporal 3518 2821 7625 2.212 0.647 0.136 0.035 46 5.5 +parahippocampal 888 572 1675 2.425 0.763 0.092 0.020 5 0.6 +paracentral 2315 1388 4190 2.762 0.727 0.097 0.023 14 2.2 +parsopercularis 2127 1536 4214 2.456 0.669 0.128 0.028 23 2.6 +parsorbitalis 1076 833 2404 2.526 0.734 0.148 0.035 15 1.6 +parstriangularis 2087 1628 4946 2.468 0.676 0.140 0.040 25 3.6 +pericalcarine 2258 1599 2304 1.634 0.414 0.143 0.037 25 3.4 +postcentral 5861 4070 8849 1.960 0.561 0.114 0.025 48 6.2 +posteriorcingulate 1769 1269 3777 2.662 0.781 0.138 0.029 22 2.2 +precentral 7650 5005 13170 2.460 0.581 0.116 0.027 58 8.8 +precuneus 5751 3950 10004 2.406 0.595 0.119 0.025 49 5.9 +rostralanteriorcingulate 827 643 2414 2.889 0.686 0.147 0.038 12 1.6 +rostralmiddlefrontal 7032 5486 15442 2.365 0.687 0.144 0.038 87 11.6 +superiorfrontal 9449 6512 22074 2.877 0.688 0.120 0.028 79 10.7 +superiorparietal 7647 5342 11973 2.044 0.551 0.125 0.025 72 7.6 +superiortemporal 5052 3778 10104 2.320 0.650 0.128 0.034 63 7.8 +supramarginal 4621 3486 8461 2.207 0.616 0.140 0.036 56 7.4 +frontalpole 372 342 1574 3.211 0.790 0.202 0.072 9 1.1 +temporalpole 582 460 2030 3.120 0.834 0.147 0.042 8 1.1 +transversetemporal 538 427 998 2.060 0.552 0.190 0.069 14 1.5 +insula 3419 2257 6398 2.765 0.876 0.129 0.041 44 6.1 diff --git a/tests/subjects/soichi/stats/rh.curv.stats b/tests/subjects/soichi/stats/rh.curv.stats new file mode 100644 index 0000000..21fff7a --- /dev/null +++ b/tests/subjects/soichi/stats/rh.curv.stats @@ -0,0 +1,220 @@ + +Raw +- (using 'rh.curv'): -0.02333 +- 0.1622 + Raw Min: -0.77579 at vertex 56974 + Raw Max: 0.59334 at vertex 110994 + Raw Curvature Calculation Type: discrete + Raw Mean Vertex Separation (Whole Surface): 0.86393 +- 0.15562 mm + Raw Total Surface Area: 79575.77344 mm^2 + Raw Total Number of Vertices: 124680 + Raw Average Vertex Area (Whole Surface): 0.63824 mm^2 + Raw Natural Surface Integral: -2091.56201 + Raw Rectified Surface Integral: 10201.73438 + Raw Positive Surface Integral: 4055.08618 + Raw Negative Surface Integral: 6146.64844 + Raw Mean Natural Surface Integral: -0.01678 across 124680 (100.00%) vertices + Raw Mean Rectified Surface Integral: 0.08182 across 124680 (100.00%) vertices + Raw Mean Positive Surface Integral: 0.06807 across 59569 (47.78%) vertices + Raw Mean Negative Surface Integral: 0.09440 across 65111 (52.22%) vertices + Raw AreaNorm Natural Surface Integral: -0.02628 across 79575.406250 (100.00%) mm^2 + Raw AreaNorm Rectified Surface Integral: 0.12820 across 79575.406250 (100.00%) mm^2 + Raw AreaNorm Positive Surface Integral: 0.11049 across 36700.890625 (46.12%) mm^2 + Raw AreaNorm Negative Surface Integral: 0.14336 across 42874.558594 (53.88%) mm^2 + +Raw +- (using 'rh.sulc'): -0.00000 +- 5.7108 + Raw Min: -13.83525 at vertex 79666 + Raw Max: 16.78419 at vertex 45579 + Raw Curvature Calculation Type: discrete + Raw Mean Vertex Separation (Whole Surface): 0.86393 +- 0.15562 mm + Raw Total Surface Area: 79575.77344 mm^2 + Raw Total Number of Vertices: 124680 + Raw Average Vertex Area (Whole Surface): 0.63824 mm^2 + Raw Natural Surface Integral: -19823.66602 + Raw Rectified Surface Integral: 370965.00000 + Raw Positive Surface Integral: 175570.67188 + Raw Negative Surface Integral: 195394.34375 + Raw Mean Natural Surface Integral: -0.15900 across 124680 (100.00%) vertices + Raw Mean Rectified Surface Integral: 2.97534 across 124680 (100.00%) vertices + Raw Mean Positive Surface Integral: 2.99353 across 58650 (47.04%) vertices + Raw Mean Negative Surface Integral: 2.95918 across 66030 (52.96%) vertices + Raw AreaNorm Natural Surface Integral: -0.24912 across 79575.406250 (100.00%) mm^2 + Raw AreaNorm Rectified Surface Integral: 4.66180 across 79575.406250 (100.00%) mm^2 + Raw AreaNorm Positive Surface Integral: 4.91655 across 35710.144531 (44.88%) mm^2 + Raw AreaNorm Negative Surface Integral: 4.45443 across 43865.214844 (55.12%) mm^2 + +K +- (using 'rh.smoothwm'): 0.02740 +- 1.0966 mm^-2 + K Min: -6.96519 at vertex 102918 + K Max: 194.38727 at vertex 102124 + K Curvature Calculation Type: discrete + K Mean Vertex Separation (Whole Surface): 0.86393 +- 0.15562 mm + K Total Surface Area: 79575.77344 mm^2 + K Total Number of Vertices: 124680 + K Average Vertex Area (Whole Surface): 0.63824 mm^2 + K Natural Surface Integral: 10.15505 + K Rectified Surface Integral: 3708.86279 + K Positive Surface Integral: 1859.50891 + K Negative Surface Integral: 1849.35388 + K Mean Natural Surface Integral: 0.00008 across 124680 (100.00%) vertices + K Mean Rectified Surface Integral: 0.02975 across 124680 (100.00%) vertices + K Mean Positive Surface Integral: 0.03242 across 57365 (46.01%) vertices + K Mean Negative Surface Integral: 0.02747 across 67315 (53.99%) vertices + K AreaNorm Natural Surface Integral: 0.00013 across 79575.406250 (100.00%) mm^2 + K AreaNorm Rectified Surface Integral: 0.04661 across 79575.406250 (100.00%) mm^2 + K AreaNorm Positive Surface Integral: 0.05666 across 32818.390625 (41.24%) mm^2 + K AreaNorm Negative Surface Integral: 0.03955 across 46756.988281 (58.76%) mm^2 + +H +- (using 'rh.smoothwm'): -0.03726 +- 0.3389 mm^-1 + H Min: -17.35979 at vertex 102124 + H Max: 9.68358 at vertex 68281 + H Curvature Calculation Type: discrete + H Mean Vertex Separation (Whole Surface): 0.86393 +- 0.15562 mm + H Total Surface Area: 79575.77344 mm^2 + H Total Number of Vertices: 124680 + H Average Vertex Area (Whole Surface): 0.63824 mm^2 + H Natural Surface Integral: -1803.74194 + H Rectified Surface Integral: 13666.22559 + H Positive Surface Integral: 5931.24219 + H Negative Surface Integral: 7734.98389 + H Mean Natural Surface Integral: -0.01447 across 124680 (100.00%) vertices + H Mean Rectified Surface Integral: 0.10961 across 124680 (100.00%) vertices + H Mean Positive Surface Integral: 0.09121 across 65026 (52.15%) vertices + H Mean Negative Surface Integral: 0.12966 across 59654 (47.85%) vertices + H AreaNorm Natural Surface Integral: -0.02267 across 79575.406250 (100.00%) mm^2 + H AreaNorm Rectified Surface Integral: 0.17174 across 79575.406250 (100.00%) mm^2 + H AreaNorm Positive Surface Integral: 0.14264 across 41582.054688 (52.25%) mm^2 + H AreaNorm Negative Surface Integral: 0.20359 across 37993.140625 (47.74%) mm^2 + +k1 +- (using 'rh.smoothwm'): -0.07581 +- 0.6173 mm^-1 + k1 Min: -28.16885 at vertex 56974 + k1 Max: 18.63453 at vertex 68281 + k1 Curvature Calculation Type: discrete + k1 Mean Vertex Separation (Whole Surface): 0.86393 +- 0.15562 mm + k1 Total Surface Area: 79575.77344 mm^2 + k1 Total Number of Vertices: 124680 + k1 Average Vertex Area (Whole Surface): 0.63824 mm^2 + k1 Natural Surface Integral: -3975.01392 + k1 Rectified Surface Integral: 28891.44336 + k1 Positive Surface Integral: 12458.21484 + k1 Negative Surface Integral: 16433.22852 + k1 Mean Natural Surface Integral: -0.03188 across 124680 (100.00%) vertices + k1 Mean Rectified Surface Integral: 0.23172 across 124680 (100.00%) vertices + k1 Mean Positive Surface Integral: 0.19159 across 65026 (52.15%) vertices + k1 Mean Negative Surface Integral: 0.27548 across 59654 (47.85%) vertices + k1 AreaNorm Natural Surface Integral: -0.04995 across 79575.406250 (100.00%) mm^2 + k1 AreaNorm Rectified Surface Integral: 0.36307 across 79575.406250 (100.00%) mm^2 + k1 AreaNorm Positive Surface Integral: 0.29961 across 41582.054688 (52.25%) mm^2 + k1 AreaNorm Negative Surface Integral: 0.43253 across 37993.140625 (47.74%) mm^2 + +k2 +- (using 'rh.smoothwm'): 0.00129 +- 0.1529 mm^-1 + k2 Min: -7.01692 at vertex 102124 + k2 Max: 2.92109 at vertex 63224 + k2 Curvature Calculation Type: discrete + k2 Mean Vertex Separation (Whole Surface): 0.86393 +- 0.15562 mm + k2 Total Surface Area: 79575.77344 mm^2 + k2 Total Number of Vertices: 124680 + k2 Average Vertex Area (Whole Surface): 0.63824 mm^2 + k2 Natural Surface Integral: 367.53009 + k2 Rectified Surface Integral: 7075.75635 + k2 Positive Surface Integral: 3721.64331 + k2 Negative Surface Integral: 3354.11328 + k2 Mean Natural Surface Integral: 0.00295 across 124680 (100.00%) vertices + k2 Mean Rectified Surface Integral: 0.05675 across 124680 (100.00%) vertices + k2 Mean Positive Surface Integral: 0.05690 across 65403 (52.46%) vertices + k2 Mean Negative Surface Integral: 0.05658 across 59277 (47.54%) vertices + k2 AreaNorm Natural Surface Integral: 0.00462 across 79575.406250 (100.00%) mm^2 + k2 AreaNorm Rectified Surface Integral: 0.08892 across 79575.406250 (100.00%) mm^2 + k2 AreaNorm Positive Surface Integral: 0.08966 across 41508.031250 (52.16%) mm^2 + k2 AreaNorm Negative Surface Integral: 0.08811 across 38067.277344 (47.84%) mm^2 + +S +- (using 'rh.smoothwm'): 0.35543 +- 3.1383 mm^-2 + S Min: 0.00000 at vertex 136 + S Max: 476.08676 at vertex 56974 + S Curvature Calculation Type: discrete + S Mean Vertex Separation (Whole Surface): 0.86393 +- 0.15562 mm + S Total Surface Area: 79575.77344 mm^2 + S Total Number of Vertices: 124680 + S Average Vertex Area (Whole Surface): 0.63824 mm^2 + S Natural Surface Integral: 20223.72461 + S Rectified Surface Integral: 20223.72461 + S Positive Surface Integral: 20223.72461 + S Negative Surface Integral: 0.00000 + S Mean Natural Surface Integral: 0.16221 across 124680 (100.00%) vertices + S Mean Rectified Surface Integral: 0.16221 across 124680 (100.00%) vertices + S Mean Positive Surface Integral: 0.16221 across 124680 (100.00%) vertices + S Mean Negative Surface Integral: 0.00000 across 0 (00.00%) vertices + S AreaNorm Natural Surface Integral: 0.25415 across 79575.406250 (100.00%) mm^2 + S AreaNorm Rectified Surface Integral: 0.25415 across 79575.406250 (100.00%) mm^2 + S AreaNorm Positive Surface Integral: 0.25415 across 79575.406250 (100.00%) mm^2 + S AreaNorm Negative Surface Integral: 0.00000 across 0.000000 (00.00%) mm^2 + +C +- (using 'rh.smoothwm'): 0.30960 +- 0.3305 mm^-2 + C Min: 0.00615 at vertex 27000 + C Max: 20.41812 at vertex 56974 + C Curvature Calculation Type: discrete + C Mean Vertex Separation (Whole Surface): 0.86393 +- 0.15562 mm + C Total Surface Area: 79575.77344 mm^2 + C Total Number of Vertices: 124680 + C Average Vertex Area (Whole Surface): 0.63824 mm^2 + C Natural Surface Integral: 21428.21484 + C Rectified Surface Integral: 21428.21484 + C Positive Surface Integral: 21428.21484 + C Negative Surface Integral: 0.00000 + C Mean Natural Surface Integral: 0.17187 across 124680 (100.00%) vertices + C Mean Rectified Surface Integral: 0.17187 across 124680 (100.00%) vertices + C Mean Positive Surface Integral: 0.17187 across 124680 (100.00%) vertices + C Mean Negative Surface Integral: 0.00000 across 0 (00.00%) vertices + C AreaNorm Natural Surface Integral: 0.26928 across 79575.406250 (100.00%) mm^2 + C AreaNorm Rectified Surface Integral: 0.26928 across 79575.406250 (100.00%) mm^2 + C AreaNorm Positive Surface Integral: 0.26928 across 79575.406250 (100.00%) mm^2 + C AreaNorm Negative Surface Integral: 0.00000 across 0.000000 (00.00%) mm^2 + +BE +- (using 'rh.smoothwm'): 0.41019 +- 5.1732 mm^-2 + BE Min: 0.00008 at vertex 27000 + BE Max: 833.79956 at vertex 56974 + BE Curvature Calculation Type: discrete + BE Mean Vertex Separation (Whole Surface): 0.86393 +- 0.15562 mm + BE Total Surface Area: 79575.77344 mm^2 + BE Total Number of Vertices: 124680 + BE Average Vertex Area (Whole Surface): 0.63824 mm^2 + BE Natural Surface Integral: 20243.11133 + BE Rectified Surface Integral: 20243.11133 + BE Positive Surface Integral: 20243.11133 + BE Negative Surface Integral: 0.00000 + BE Mean Natural Surface Integral: 0.16236 across 124680 (100.00%) vertices + BE Mean Rectified Surface Integral: 0.16236 across 124680 (100.00%) vertices + BE Mean Positive Surface Integral: 0.16236 across 124680 (100.00%) vertices + BE Mean Negative Surface Integral: 0.00000 across 0 (00.00%) vertices + BE AreaNorm Natural Surface Integral: 0.25439 across 79575.406250 (100.00%) mm^2 + BE AreaNorm Rectified Surface Integral: 0.25439 across 79575.406250 (100.00%) mm^2 + BE AreaNorm Positive Surface Integral: 0.25439 across 79575.406250 (100.00%) mm^2 + BE AreaNorm Negative Surface Integral: 0.00000 across 0.000000 (00.00%) mm^2 + +FI +- (using 'rh.smoothwm'): 0.31279 +- 3.8860 mm^-2 + FI Min: 0.00000 at vertex 136 + FI Max: 614.62775 at vertex 56974 + FI Curvature Calculation Type: discrete + FI Mean Vertex Separation (Whole Surface): 0.86393 +- 0.15562 mm + FI Total Surface Area: 79575.77344 mm^2 + FI Total Number of Vertices: 124680 + FI Average Vertex Area (Whole Surface): 0.63824 mm^2 + FI Natural Surface Integral: 15214.53516 + FI Rectified Surface Integral: 15214.53516 + FI Positive Surface Integral: 15214.53516 + FI Negative Surface Integral: 0.00000 + FI Mean Natural Surface Integral: 0.12203 across 124680 (100.00%) vertices + FI Mean Rectified Surface Integral: 0.12203 across 124680 (100.00%) vertices + FI Mean Positive Surface Integral: 0.12203 across 124680 (100.00%) vertices + FI Mean Negative Surface Integral: 0.00000 across 0 (00.00%) vertices + FI AreaNorm Natural Surface Integral: 0.19120 across 79575.406250 (100.00%) mm^2 + FI AreaNorm Rectified Surface Integral: 0.19120 across 79575.406250 (100.00%) mm^2 + FI AreaNorm Positive Surface Integral: 0.19120 across 79575.406250 (100.00%) mm^2 + FI AreaNorm Negative Surface Integral: 0.00000 across 0.000000 (00.00%) mm^2 + +curv -- calculation type: discrete +curv -- Folding Index (FI): 1210.73425 +curv -- Intrinsic Curvature Index - positive (ICIp): 147.97502 +curv -- Intrinsic Curvature Index - negative (ICIn): 147.16690 +curv -- Intrinsic Curvature Index - natural (ICIt): 0.80811 + +Mean across 10 curvatures: 1.2803e-01 +- 1.8243e-01 + + diff --git a/tests/subjects/soichi/stats/rh.w-g.pct.stats b/tests/subjects/soichi/stats/rh.w-g.pct.stats new file mode 100644 index 0000000..7e975b3 --- /dev/null +++ b/tests/subjects/soichi/stats/rh.w-g.pct.stats @@ -0,0 +1,92 @@ +# Title Segmentation Statistics +# +# generating_program mri_segstats +# cvs_version 7.0.0 +# cmdline mri_segstats --in /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f/output/surf/rh.w-g.pct.mgh --annot output rh aparc --sum /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f/output/stats/rh.w-g.pct.stats --snr +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# anatomy_type surface +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# subjectname output +# Annot output rh aparc +# ColorTable /tmp/mri_segstats.tmp.output.rh.176.ctab +# ColorTableTimeStamp 2020/05/04 22:13:42 +# InVolFile /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f/output/surf/rh.w-g.pct.mgh +# InVolFileTimeStamp 2020/05/04 22:13:41 +# InVolFrame 0 +# Only reporting non-empty segmentations +# VertexArea_mm2 0.713817 +# TableCol 1 ColHeader Index +# TableCol 1 FieldName Index +# TableCol 1 Units NA +# TableCol 2 ColHeader SegId +# TableCol 2 FieldName Segmentation Id +# TableCol 2 Units NA +# TableCol 3 ColHeader NVertices +# TableCol 3 FieldName Number of Vertices +# TableCol 3 Units unitless +# TableCol 4 ColHeader Area_mm2 +# TableCol 4 FieldName Area +# TableCol 4 Units mm^2 +# TableCol 5 ColHeader StructName +# TableCol 5 FieldName Structure Name +# TableCol 5 Units NA +# TableCol 6 ColHeader Mean +# TableCol 6 FieldName Intensity Mean +# TableCol 6 Units unknown +# TableCol 7 ColHeader StdDev +# TableCol 7 FieldName Itensity StdDev +# TableCol 7 Units unknown +# TableCol 8 ColHeader Min +# TableCol 8 FieldName Intensity Min +# TableCol 8 Units unknown +# TableCol 9 ColHeader Max +# TableCol 9 FieldName Intensity Max +# TableCol 9 Units unknown +# TableCol 10 ColHeader Range +# TableCol 10 FieldName Intensity Range +# TableCol 10 Units unknown +# TableCol 11 ColHeader SNR +# TableCol 11 FieldName Intensity SNR +# TableCol 11 Units none +# NRows 35 +# NTableCols 11 +# ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range SNR + 1 2000 8853 5420.3 unknown 0.0000 0.0000 0.0000 0.0000 0.0000 -nan + 2 2001 1094 756.7 bankssts 31.2677 7.1936 -1.4849 50.0722 51.5571 4.3466 + 3 2002 1137 779.6 caudalanteriorcingulate 30.7286 7.7858 7.1339 50.1157 42.9818 3.9468 + 4 2003 3126 2217.6 caudalmiddlefrontal 29.0918 6.1220 3.0490 48.5092 45.4603 4.7520 + 5 2005 2446 1781.0 cuneus 24.3815 5.9971 3.7057 41.9099 38.2042 4.0655 + 6 2006 448 310.1 entorhinal 29.2989 7.7223 -3.7783 54.4055 58.1838 3.7941 + 7 2007 3194 2329.9 fusiform 28.7824 7.7527 -9.2600 52.1709 61.4310 3.7126 + 8 2008 7290 5466.7 inferiorparietal 29.2785 7.0142 -26.9370 57.2965 84.2335 4.1742 + 9 2009 2872 2202.8 inferiortemporal 30.1240 8.4380 0.6067 55.0641 54.4574 3.5700 + 10 2010 1455 1084.6 isthmuscingulate 24.6425 8.0622 -6.1244 56.7026 62.8269 3.0566 + 11 2011 6205 4673.5 lateraloccipital 26.6143 7.6781 -9.8784 56.7037 66.5822 3.4663 + 12 2012 3755 2748.3 lateralorbitofrontal 28.4431 11.1385 -52.8371 74.9205 127.7576 2.5536 + 13 2013 4863 3579.3 lingual 23.9671 8.3827 -57.4021 45.5011 102.9032 2.8591 + 14 2014 3103 2244.0 medialorbitofrontal 28.9179 11.5042 -56.8839 54.1360 111.0199 2.5137 + 15 2015 3518 2820.8 middletemporal 27.5033 7.7895 -9.8213 54.8879 64.7092 3.5308 + 16 2016 888 571.8 parahippocampal 30.4945 7.8268 -1.3078 63.7504 65.0582 3.8961 + 17 2017 2315 1388.4 paracentral 24.0975 8.5854 -0.1541 42.9093 43.0634 2.8068 + 18 2018 2127 1536.2 parsopercularis 30.6128 7.3398 -10.2121 53.0001 63.2122 4.1708 + 19 2019 1076 832.6 parsorbitalis 28.4238 7.5325 2.9583 51.4170 48.4587 3.7735 + 20 2020 2087 1627.5 parstriangularis 28.4401 7.1978 1.5305 54.2725 52.7420 3.9512 + 21 2021 2258 1599.5 pericalcarine 22.1914 5.8634 -0.6005 38.1512 38.7517 3.7847 + 22 2022 5861 4069.8 postcentral 26.5326 6.3235 -6.1775 52.9131 59.0906 4.1959 + 23 2023 1769 1269.1 posteriorcingulate 29.5282 9.0183 4.1041 56.4376 52.3334 3.2743 + 24 2024 7650 5005.2 precentral 24.8604 7.6613 -9.0372 56.5383 65.5754 3.2449 + 25 2025 5751 3949.9 precuneus 29.1653 6.5867 2.7738 56.3786 53.6048 4.4279 + 26 2026 827 643.2 rostralanteriorcingulate 28.5428 7.9780 5.7940 59.9231 54.1290 3.5777 + 27 2027 7032 5486.2 rostralmiddlefrontal 28.8678 7.3535 -8.7395 50.9992 59.7387 3.9257 + 28 2028 9449 6511.7 superiorfrontal 30.5148 6.8143 3.1892 55.3544 52.1653 4.4780 + 29 2029 7647 5341.8 superiorparietal 28.2989 5.9352 -4.5147 47.7949 52.3096 4.7680 + 30 2030 5052 3777.7 superiortemporal 29.3703 8.2497 -56.9813 64.5267 121.5080 3.5602 + 31 2031 4621 3486.1 supramarginal 29.2036 7.8452 -28.3112 53.0074 81.3186 3.7225 + 32 2032 372 341.7 frontalpole 29.1104 8.2514 9.4101 49.6567 40.2466 3.5279 + 33 2033 582 460.2 temporalpole 27.7395 9.2680 -12.6508 54.7236 67.3745 2.9930 + 34 2034 538 427.5 transversetemporal 22.7135 9.2696 -37.0885 53.3634 90.4520 2.4503 + 35 2035 3419 2257.4 insula 25.0075 14.1123 -69.1953 96.5754 165.7708 1.7720 diff --git a/tests/subjects/soichi/stats/wmparc.stats b/tests/subjects/soichi/stats/wmparc.stats new file mode 100644 index 0000000..d0ad3ef --- /dev/null +++ b/tests/subjects/soichi/stats/wmparc.stats @@ -0,0 +1,135 @@ +# Title Segmentation Statistics +# +# generating_program mri_segstats +# cvs_version 7.0.0 +# cmdline mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject output --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv +# sysname Linux +# hostname nid00762 +# machine x86_64 +# user hayashis +# anatomy_type volume +# +# SUBJECTS_DIR /N/dc2/scratch/hayashis/bigred3-workflows/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f +# subjectname output +# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3 +# Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 9296.000000, mm^3 +# Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 251589.500000, mm^3 +# Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 244895.500000, mm^3 +# Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 496485.000000, mm^3 +# Measure Mask, MaskVol, Mask Volume, 1686052.000000, mm^3 +# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1420434.160521, mm^3 +# SegVolFile mri/wmparc.mgz +# SegVolFileTimeStamp 2020/05/04 22:17:18 +# ColorTable /usr/local/freesurfer/WMParcStatsLUT.txt +# ColorTableTimeStamp 2020/04/29 22:19:19 +# InVolFile mri/norm.mgz +# InVolFileTimeStamp 2020/05/04 19:28:46 +# InVolFrame 0 +# PVVolFile mri/norm.mgz +# PVVolFileTimeStamp 2020/05/04 19:28:46 +# ExcludeSegId 0 +# Only reporting non-empty segmentations +# VoxelVolume_mm3 1 +# TableCol 1 ColHeader Index +# TableCol 1 FieldName Index +# TableCol 1 Units NA +# TableCol 2 ColHeader SegId +# TableCol 2 FieldName Segmentation Id +# TableCol 2 Units NA +# TableCol 3 ColHeader NVoxels +# TableCol 3 FieldName Number of Voxels +# TableCol 3 Units unitless +# TableCol 4 ColHeader Volume_mm3 +# TableCol 4 FieldName Volume +# TableCol 4 Units mm^3 +# TableCol 5 ColHeader StructName +# TableCol 5 FieldName Structure Name +# TableCol 5 Units NA +# TableCol 6 ColHeader normMean +# TableCol 6 FieldName Intensity normMean +# TableCol 6 Units MR +# TableCol 7 ColHeader normStdDev +# TableCol 7 FieldName Itensity normStdDev +# TableCol 7 Units MR +# TableCol 8 ColHeader normMin +# TableCol 8 FieldName Intensity normMin +# TableCol 8 Units MR +# TableCol 9 ColHeader normMax +# TableCol 9 FieldName Intensity normMax +# TableCol 9 Units MR +# TableCol 10 ColHeader normRange +# TableCol 10 FieldName Intensity normRange +# TableCol 10 Units MR +# NRows 70 +# NTableCols 10 +# ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange + 1 3001 2601 2512.0 wm-lh-bankssts 97.0035 9.7451 68.0000 114.0000 46.0000 + 2 3002 2569 2546.1 wm-lh-caudalanteriorcingulate 101.8139 8.1896 74.0000 119.0000 45.0000 + 3 3003 7450 7223.8 wm-lh-caudalmiddlefrontal 94.9421 10.7322 65.0000 114.0000 49.0000 + 4 3005 3369 3259.8 wm-lh-cuneus 94.9332 10.4060 69.0000 117.0000 48.0000 + 5 3006 812 861.8 wm-lh-entorhinal 80.1010 8.2502 50.0000 106.0000 56.0000 + 6 3007 5824 5518.4 wm-lh-fusiform 88.3800 11.4213 37.0000 114.0000 77.0000 + 7 3008 9490 9347.7 wm-lh-inferiorparietal 97.8016 11.3678 67.0000 120.0000 53.0000 + 8 3009 6336 6183.9 wm-lh-inferiortemporal 87.1286 12.3249 46.0000 115.0000 69.0000 + 9 3010 3865 3816.4 wm-lh-isthmuscingulate 100.3868 8.7188 48.0000 115.0000 67.0000 + 10 3011 11004 10674.5 wm-lh-lateraloccipital 88.3762 11.5626 60.0000 113.0000 53.0000 + 11 3012 7085 6924.7 wm-lh-lateralorbitofrontal 93.0385 10.5048 65.0000 111.0000 46.0000 + 12 3013 6295 6109.3 wm-lh-lingual 88.7207 11.9893 33.0000 116.0000 83.0000 + 13 3014 4042 3921.5 wm-lh-medialorbitofrontal 88.1319 11.2105 28.0000 110.0000 82.0000 + 14 3015 4263 4162.3 wm-lh-middletemporal 82.0263 10.3133 60.0000 113.0000 53.0000 + 15 3016 1488 1537.2 wm-lh-parahippocampal 89.2776 8.3251 65.0000 111.0000 46.0000 + 16 3017 4833 4766.4 wm-lh-paracentral 96.0341 8.7242 70.0000 112.0000 42.0000 + 17 3018 4449 4318.2 wm-lh-parsopercularis 97.8932 11.9277 66.0000 121.0000 55.0000 + 18 3019 1013 1021.9 wm-lh-parsorbitalis 86.1244 10.0806 66.0000 112.0000 46.0000 + 19 3020 3476 3438.2 wm-lh-parstriangularis 93.2221 11.4279 65.0000 116.0000 51.0000 + 20 3021 4297 3997.9 wm-lh-pericalcarine 92.4010 10.9981 64.0000 115.0000 51.0000 + 21 3022 8914 8713.7 wm-lh-postcentral 90.4774 11.1922 64.0000 120.0000 56.0000 + 22 3023 4922 4771.9 wm-lh-posteriorcingulate 99.0494 9.6038 40.0000 120.0000 80.0000 + 23 3024 15816 15460.2 wm-lh-precentral 93.3146 10.5833 63.0000 123.0000 60.0000 + 24 3025 9693 9512.1 wm-lh-precuneus 101.0122 10.4053 34.0000 123.0000 89.0000 + 25 3026 2855 2721.7 wm-lh-rostralanteriorcingulate 94.9534 11.9133 34.0000 124.0000 90.0000 + 26 3027 13505 13250.9 wm-lh-rostralmiddlefrontal 95.2532 10.9045 66.0000 119.0000 53.0000 + 27 3028 21614 21321.0 wm-lh-superiorfrontal 94.7018 9.7207 67.0000 112.0000 45.0000 + 28 3029 11851 11705.4 wm-lh-superiorparietal 98.2010 10.5361 66.0000 118.0000 52.0000 + 29 3030 8058 8129.2 wm-lh-superiortemporal 91.7812 12.2055 63.0000 115.0000 52.0000 + 30 3031 9710 9452.1 wm-lh-supramarginal 95.3726 12.1487 65.0000 125.0000 60.0000 + 31 3032 359 364.5 wm-lh-frontalpole 90.1643 9.6661 68.0000 109.0000 41.0000 + 32 3033 760 802.4 wm-lh-temporalpole 77.0237 9.3545 60.0000 101.0000 41.0000 + 33 3034 767 739.9 wm-lh-transversetemporal 91.7301 8.4409 72.0000 109.0000 37.0000 + 34 3035 9915 9690.0 wm-lh-insula 95.9767 10.7506 35.0000 123.0000 88.0000 + 35 4001 2477 2401.1 wm-rh-bankssts 97.5902 10.3221 67.0000 115.0000 48.0000 + 36 4002 2978 2936.1 wm-rh-caudalanteriorcingulate 101.4993 8.7541 73.0000 115.0000 42.0000 + 37 4003 6672 6445.6 wm-rh-caudalmiddlefrontal 94.9323 11.6110 66.0000 114.0000 48.0000 + 38 4005 3358 3218.5 wm-rh-cuneus 92.9506 9.8817 66.0000 115.0000 49.0000 + 39 4006 575 617.5 wm-rh-entorhinal 79.6104 8.6196 26.0000 103.0000 77.0000 + 40 4007 5446 5253.8 wm-rh-fusiform 90.3671 11.7024 48.0000 116.0000 68.0000 + 41 4008 12476 12185.4 wm-rh-inferiorparietal 96.6652 12.2178 65.0000 120.0000 55.0000 + 42 4009 5183 5045.3 wm-rh-inferiortemporal 87.3704 11.9947 62.0000 114.0000 52.0000 + 43 4010 3589 3570.8 wm-rh-isthmuscingulate 99.5138 8.6139 62.0000 115.0000 53.0000 + 44 4011 10090 9880.6 wm-rh-lateraloccipital 89.2856 12.2495 59.0000 117.0000 58.0000 + 45 4012 7123 6954.3 wm-rh-lateralorbitofrontal 90.4810 10.7228 59.0000 121.0000 62.0000 + 46 4013 7628 7390.5 wm-rh-lingual 90.9744 12.0386 41.0000 119.0000 78.0000 + 47 4014 4796 4797.5 wm-rh-medialorbitofrontal 91.9018 11.5839 33.0000 114.0000 81.0000 + 48 4015 5526 5409.9 wm-rh-middletemporal 84.8498 12.3874 61.0000 114.0000 53.0000 + 49 4016 1530 1585.4 wm-rh-parahippocampal 88.8752 8.7194 63.0000 112.0000 49.0000 + 50 4017 4810 4777.9 wm-rh-paracentral 96.4100 8.0507 68.0000 113.0000 45.0000 + 51 4018 3987 3883.2 wm-rh-parsopercularis 96.6850 11.3934 67.0000 122.0000 55.0000 + 52 4019 1402 1407.7 wm-rh-parsorbitalis 85.9544 9.8816 65.0000 108.0000 43.0000 + 53 4020 3854 3755.4 wm-rh-parstriangularis 92.6925 10.3468 68.0000 113.0000 45.0000 + 54 4021 4223 3869.1 wm-rh-pericalcarine 90.5816 10.6563 63.0000 114.0000 51.0000 + 55 4022 8399 8231.8 wm-rh-postcentral 89.8393 11.6256 64.0000 122.0000 58.0000 + 56 4023 4588 4445.1 wm-rh-posteriorcingulate 97.7411 9.3550 50.0000 116.0000 66.0000 + 57 4024 15235 14898.2 wm-rh-precentral 92.2593 10.6239 64.0000 119.0000 55.0000 + 58 4025 10761 10524.1 wm-rh-precuneus 99.7908 10.6824 67.0000 119.0000 52.0000 + 59 4026 1877 1817.0 wm-rh-rostralanteriorcingulate 95.3676 9.9165 71.0000 116.0000 45.0000 + 60 4027 12977 12701.9 wm-rh-rostralmiddlefrontal 94.7818 11.0499 66.0000 115.0000 49.0000 + 61 4028 17902 17618.1 wm-rh-superiorfrontal 94.4570 10.4738 65.0000 114.0000 49.0000 + 62 4029 11361 11202.5 wm-rh-superiorparietal 95.0116 11.2582 65.0000 119.0000 54.0000 + 63 4030 7064 7065.3 wm-rh-superiortemporal 90.3657 12.2806 61.0000 143.0000 82.0000 + 64 4031 9127 8863.9 wm-rh-supramarginal 95.2955 12.7435 63.0000 119.0000 56.0000 + 65 4032 501 514.3 wm-rh-frontalpole 92.9281 9.9839 73.0000 115.0000 42.0000 + 66 4033 756 780.1 wm-rh-temporalpole 77.0952 7.9339 61.0000 102.0000 41.0000 + 67 4034 510 475.5 wm-rh-transversetemporal 91.9157 8.9136 70.0000 124.0000 54.0000 + 68 4035 9430 9250.4 wm-rh-insula 95.7054 10.6164 66.0000 129.0000 63.0000 + 69 5001 35796 36106.6 Left-UnsegmentedWhiteMatter 100.5774 11.3327 22.0000 128.0000 106.0000 + 70 5002 34191 34670.3 Right-UnsegmentedWhiteMatter 101.1939 9.5786 35.0000 122.0000 87.0000