Hi Freesurfer team, Thank you in advance for your help. We are attempting to obtain left hemisphere and right hemisphere volumes for various grey and white matter structures in a variety of controls and brain injured patients. However, values for the corpus callosum are often not reported in aparc.stats files for either hemisphere. This has occurred for both patients and normal controls. Is there a reason why these values are not being computed?
Also, in the aseg.stats for several patients, the Corpus Callosum mean values are reported as 0.0000 with SD, Min, and Max of 0 as well. Are the brains perhaps too structurally abnormal to report a reliable value? The subjects with this problem had a ventriculostomy, which damaged the corpus callosum to some extent. Should CC values for these patients be considered unusable? I have attached a T1-hdr file for your reference. In addition, I have attached the aseg.stats file for this subject(which reports a CC value of 0) and the lh.aparc.stats file (which did not report a corpus callosum value). If the ventriculostomy is to blame, can you provide a reason why for some normal controls the corpus callosum volume was not calculated for left and right hemispheres? Any insight you could provide would be greatly appreciated. Thank you very much for your time and help, Matt
St5B-T1.hdr
Description: St5B-T1.hdr
# Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.20 2006/07/31 21:56:54 greve Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject St5-Rescan --ctab /Applications/freesurfer/ASegStatsLUT.txt # anatomy_type volume # # BrainMaskFile mri/brainmask.mgz # BrainMaskFileTimeStamp 2007/19/10 15:49:01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1767972, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1767972.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1419930, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1419930.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1418598.542711, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2007/20/10 02:25:35 # ColorTable /Applications/freesurfer/ASegStatsLUT.txt # ColorTableTimeStamp 2006/30/09 13:45:29 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2007/19/10 16:35:29 # InVolFrame 0 # PVVolFile mri/norm.mgz # PVVolFileTimeStamp 2007/19/10 16:35:29 # ExcludeSegId 0 # 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 48 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 2 258032 258032.0 Left-Cerebral-White-Matter 108.5969 7.9733 35.0000 192.0000 157.0000 2 3 319891 319891.0 Left-Cerebral-Cortex 82.2331 11.0305 31.0000 181.0000 150.0000 3 4 6403 6403.0 Left-Lateral-Ventricle 45.5700 12.5943 19.0000 88.0000 69.0000 4 5 795 795.0 Left-Inf-Lat-Vent 56.7010 16.0756 23.0000 98.0000 75.0000 5 7 17463 17463.0 Left-Cerebellum-White-Matter 94.6489 7.2514 41.0000 125.0000 84.0000 6 8 57382 57382.0 Left-Cerebellum-Cortex 77.9218 11.1002 28.0000 196.0000 168.0000 7 10 7420 7420.0 Left-Thalamus-Proper 96.5092 8.6714 58.0000 121.0000 63.0000 8 11 3078 3078.0 Left-Caudate 93.4770 9.2975 56.0000 125.0000 69.0000 9 12 5248 5248.0 Left-Putamen 95.2749 6.5034 61.0000 115.0000 54.0000 10 13 1114 1114.0 Left-Pallidum 111.6038 8.2461 89.0000 131.0000 42.0000 11 14 1345 1345.0 3rd-Ventricle 52.4789 11.3651 21.0000 85.0000 64.0000 12 15 2594 2594.0 4th-Ventricle 48.8474 8.3808 27.0000 77.0000 50.0000 13 16 20586 20586.0 Brain-Stem 90.9104 10.9212 34.0000 117.0000 83.0000 14 17 4937 4937.0 Left-Hippocampus 80.7524 8.3257 43.0000 108.0000 65.0000 15 18 1704 1704.0 Left-Amygdala 81.3604 7.5608 50.0000 106.0000 56.0000 16 24 2118 2118.0 CSF 60.6056 13.7005 24.0000 101.0000 77.0000 17 26 669 669.0 Left-Accumbens-area 85.8443 6.3001 63.0000 114.0000 51.0000 18 28 4007 4007.0 Left-VentralDC 96.5894 10.9231 49.0000 124.0000 75.0000 19 30 78 78.0 Left-vessel 76.4930 12.2636 50.0000 102.0000 52.0000 20 31 0 0.0 Left-choroid-plexus 0.0000 0.0000 0.0000 0.0000 0.0000 21 41 276320 276320.0 Right-Cerebral-White-Matter 110.4005 8.2597 44.0000 170.0000 126.0000 22 42 315288 315288.0 Right-Cerebral-Cortex 84.0824 10.8264 0.0000 178.0000 178.0000 23 43 9241 9241.0 Right-Lateral-Ventricle 45.3153 13.4594 19.0000 98.0000 79.0000 24 44 222 222.0 Right-Inf-Lat-Vent 57.0602 12.7758 29.0000 95.0000 66.0000 25 46 13535 13535.0 Right-Cerebellum-White-Matter 95.4856 5.8509 50.0000 140.0000 90.0000 26 47 59673 59673.0 Right-Cerebellum-Cortex 81.4773 10.7986 32.0000 170.0000 138.0000 27 49 6949 6949.0 Right-Thalamus-Proper 96.2021 9.3082 52.0000 121.0000 69.0000 28 50 4103 4103.0 Right-Caudate 89.4463 8.7990 51.0000 113.0000 62.0000 29 51 4891 4891.0 Right-Putamen 101.4397 6.5465 73.0000 118.0000 45.0000 30 52 1816 1816.0 Right-Pallidum 114.0245 5.7157 95.0000 131.0000 36.0000 31 53 5000 5000.0 Right-Hippocampus 78.1196 9.1730 45.0000 104.0000 59.0000 32 54 1528 1528.0 Right-Amygdala 81.2189 6.9702 56.0000 101.0000 45.0000 33 58 799 799.0 Right-Accumbens-area 87.0969 5.5732 64.0000 104.0000 40.0000 34 60 4659 4659.0 Right-VentralDC 97.7320 11.2039 48.0000 128.0000 80.0000 35 62 68 68.0 Right-vessel 76.8214 11.8799 53.0000 99.0000 46.0000 36 72 118 118.0 5th-Ventricle 62.7755 7.0001 46.0000 82.0000 36.0000 37 77 0 0.0 WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 38 78 1257 1257.0 Left-WM-hypointensities 81.1010 16.4823 34.0000 117.0000 83.0000 39 79 911 911.0 Right-WM-hypointensities 81.9619 13.5290 32.0000 110.0000 78.0000 40 80 0 0.0 non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 41 81 5 5.0 Left-non-WM-hypointensities 66.5714 11.9004 49.0000 85.0000 36.0000 42 82 0 0.0 Right-non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 43 85 301 301.0 Optic-Chiasm 76.6491 13.5073 44.0000 104.0000 60.0000 44 251 0 0.0 CC_Posterior 0.0000 0.0000 0.0000 0.0000 0.0000 45 252 0 0.0 CC_Mid_Posterior 0.0000 0.0000 0.0000 0.0000 0.0000 46 253 0 0.0 CC_Central 0.0000 0.0000 0.0000 0.0000 0.0000 47 254 0 0.0 CC_Mid_Anterior 0.0000 0.0000 0.0000 0.0000 0.0000 48 255 0 0.0 CC_Anterior 0.0000 0.0000 0.0000 0.0000 0.0000
# Table of FreeSurfer cortical parcellation anatomical statistics # # CreationTime 2008/02/29-20:08:20-GMT # generating_program mris_anatomical_stats # cvs_version $Id: mris_anatomical_stats.c,v 1.54 2007/08/02 17:37:13 nicks Exp $ # mrisurf.c-cvs_version $Id: mrisurf.c,v 1.557.2.5 2007/12/10 20:20:29 nicks Exp $ # cmdline mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab St5-Rescan lh # # anatomy_type surface # hemi lh # AnnotationFile ../label/lh.aparc.annot # AnnotationFileTimeStamp 2008/02/29 14:07:55 # Measure Cortex, NumVert, Number of Vertices, 163622, unitless # Measure Cortex, SurfArea, Surface Area, 101781, mm^2 # 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 unknown 11827 7812 14176 1.758 1.639 0.162 0.215 954 92.3 bankssts 2005 1375 3829 2.881 0.656 0.127 0.036 23 3.1 caudalanteriorcingulate 916 575 2270 3.174 0.956 0.163 0.079 19 3.1 caudalmiddlefrontal 3535 2031 5092 2.422 0.613 0.126 0.192 454 15.6 cuneus 2963 1913 3609 1.919 0.570 0.187 0.186 96 19.4 entorhinal 481 319 1278 2.881 0.728 0.201 0.116 16 2.9 fusiform 4567 3111 9455 2.631 0.722 0.162 0.087 261 15.6 inferiorparietal 9107 5494 15868 2.640 0.693 0.147 0.096 600 39.6 inferiortemporal 6470 4121 14340 2.769 0.909 0.177 0.191 276 54.9 isthmuscingulate 1020 673 2342 3.176 0.830 0.172 0.073 23 3.0 lateraloccipital 10383 6491 15553 2.286 0.778 0.163 0.087 355 39.3 lateralorbitofrontal 4991 3364 9158 2.681 0.744 0.182 0.098 126 22.0 lingual 5140 3407 8189 2.280 0.705 0.168 0.085 122 19.2 medialorbitofrontal 2880 1941 6211 2.792 0.744 0.180 0.116 89 13.0 middletemporal 5648 3731 14696 3.125 0.760 0.140 0.067 107 15.0 parahippocampal 1064 688 2277 2.813 0.847 0.135 0.071 14 3.2 paracentral 2652 1582 3921 2.233 0.652 0.143 0.108 142 12.8 parsopercularis 2969 1788 6121 2.955 0.677 0.143 0.090 62 10.4 parsorbitalis 1222 763 2705 2.797 0.784 0.206 0.393 420 29.2 parstriangularis 3119 1864 5419 2.587 0.678 0.150 0.246 425 26.2 pericalcarine 2769 1784 2581 1.628 0.557 0.163 0.130 79 11.0 postcentral 6516 3956 8642 1.956 0.797 0.126 0.055 92 14.8 posteriorcingulate 1701 1195 3747 2.820 0.643 0.158 0.067 37 4.8 precentral 8198 4715 13342 2.597 0.600 0.124 0.077 362 29.9 precuneus 6773 4373 11306 2.343 0.663 0.143 0.074 128 19.1 rostralanteriorcingulate 1131 721 2601 2.994 0.990 0.161 0.209 79 4.8 rostralmiddlefrontal 13460 7832 21597 2.458 0.676 0.161 0.156 1244 86.3 superiorfrontal 13561 8068 23478 2.646 0.741 0.144 0.099 378 47.6 superiorparietal 11408 6640 14920 2.085 0.624 0.135 0.072 470 34.6 superiortemporal 6550 4103 13896 2.878 0.685 0.142 0.177 427 24.3 supramarginal 6616 4143 12548 2.697 0.693 0.134 0.061 163 18.0 frontalpole 456 246 666 2.123 0.972 0.191 0.124 13 2.7 temporalpole 712 511 1863 2.839 0.914 0.277 0.606 65 10.3 transversetemporal 812 452 1307 2.674 0.370 0.128 0.067 12 2.7
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