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# cmdline mri_segstats --seg /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v4/mri/aparc+aseg.mgz --ctab /home/nmrclass/freesurfer/FreeSurferColorLUT.txt --id 1021 --id 1022 --id 1030 --id 17 --i ces.anat.bb.mgh --sum ces.abs-masked.bb.stats --mask sig.anat.bb.mgh --maskthresh 2 --masksign abs # cmdline mri_segstats --seg /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/aparc+aseg.mgz --ctab /home/nmrclass/freesurfer/FreeSurferColorLUT.txt --id 1021 --id 1022 --id 1030 --id 17 --i ces.anat.bb.mgh --sum ces.abs-masked.bb.stats --mask sig.anat.bb.mgh --maskthresh 2 --masksign abs
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# hostname nmrclass # hostname nmrclass33
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# SegVolFile /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v4/mri/aparc+aseg.mgz # SegVolFile /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/aparc+aseg.mgz
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# MaskVolFileTimeStamp 2017/02/10 22:48:43 # MaskVolFileTimeStamp 2018/02/21 13:09:26
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# InVolFileTimeStamp 2017/02/10 22:38:30 # InVolFileTimeStamp 2018/02/21 12:17:20
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  1 1021 1535 1535.0 ctx-lh-pericalcarine 180.1391 163.3732 -93.9361 713.9155 807.8517
  2 1022 5937 5937.0 ctx-lh-postcentral 60.8179 100.6084 -232.6694 461.8479 694.5173
  3 1030 5012 5012.0 ctx-lh-superiortemporal 88.2699 100.3035 -143.5521 461.8479 605.4000
  4 17 136 136.0 Left-Hippocampus 26.6048 62.5893 -113.9432 131.5358 245.4790
  1 1021 1530 1530.0 ctx-lh-pericalcarine 182.5064 164.3479 -111.9001 713.9155 825.8157
  2 1022 5935 5935.0 ctx-lh-postcentral 60.9178 100.7243 -232.6694 461.8479 694.5173
  3 1030 5020 5020.0 ctx-lh-superiortemporal 89.1554 100.8434 -143.5521 461.8479 605.4000
  4 17 136 136.0 Left-Hippocampus 24.2060 63.0450 -113.9432 131.5358 245.4790
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# cmdline mri_segstats --seg /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v4/mri/aparc+aseg.mgz --ctab /home/nmrclass/freesurfer/FreeSurferColorLUT.txt --id 1021 --id 1022 --id 1030 --id 17 --i ces.anat.bb.mgh --sum ces.pos-masked.bb.stats --mask sig.anat.bb.mgh --maskthresh 2 --masksign pos # cmdline mri_segstats --seg /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/aparc+aseg.mgz --ctab /home/nmrclass/freesurfer/FreeSurferColorLUT.txt --id 1021 --id 1022 --id 1030 --id 17 --i ces.anat.bb.mgh --sum ces.pos-masked.bb.stats --mask sig.anat.bb.mgh --maskthresh 2 --masksign pos
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# hostname nmrclass # hostname nmrclass33
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# SegVolFile /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v4/mri/aparc+aseg.mgz # SegVolFile /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/aparc+aseg.mgz
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# MaskVolFileTimeStamp 2017/02/10 22:56:48 # MaskVolFileTimeStamp 2018/02/21 13:13:42
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# InVolFileTimeStamp 2017/02/10 22:38:30 # InVolFileTimeStamp 2018/02/21 12:17:20
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  1 1021 1424 1424.0 ctx-lh-pericalcarine 198.5072 155.1710 32.1526 713.9155 681.7629
  2 1022 4339 4339.0 ctx-lh-postcentral 107.5108 72.4555 19.5321 461.8479 442.3158
  3 1030 4283 4283.0 ctx-lh-superiortemporal 111.8215 88.4794 25.4251 461.8479 436.4228
  4 17 79 79.0 Left-Hippocampus 75.6666 28.8688 43.2457 131.5358 88.2900
  1 1021 1422 1422.0 ctx-lh-pericalcarine 200.5127 156.3413 32.1526 713.9155 681.7629
  2 1022 4340 4340.0 ctx-lh-postcentral 107.5646 72.6399 19.5321 461.8479 442.3158
  3 1030 4300 4300.0 ctx-lh-superiortemporal 112.4998 89.1221 25.4251 461.8479 436.4228
  4 17 77 77.0 Left-Hippocampus 75.2143 28.8035 43.2457 131.5358 88.2900

ces.bb.stats

# Title Segmentation Statistics 
# 
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
# cmdline mri_segstats --seg /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/aparc+aseg.mgz --ctab /home/nmrclass/freesurfer/FreeSurferColorLUT.txt --id 1021 --id 1022 --id 1030 --id 17 --i ces.anat.bb.mgh --sum ces.bb.stats 
# sysname  Linux
# hostname nmrclass33
# machine  x86_64
# user     nmrclass
# anatomy_type volume
# 
# SegVolFile /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/aparc+aseg.mgz 
# SegVolFileTimeStamp  2017/02/08 11:13:38 
# ColorTable /home/nmrclass/freesurfer/FreeSurferColorLUT.txt 
# ColorTableTimeStamp 2017/01/18 17:00:02 
# InVolFile  ces.anat.bb.mgh 
# InVolFileTimeStamp  2018/02/21 12:17:20 
# InVolFrame 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 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
# NRows 4 
# NTableCols 10 
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range  
  1 1021      2752     2752.0  ctx-lh-pericalcarine             107.7495   149.3924  -111.9001   713.9155   825.8157 
  2 1022     12433    12433.0  ctx-lh-postcentral                27.4394    78.9434  -232.6694   461.8479   694.5173 
  3 1030     14850    14850.0  ctx-lh-superiortemporal           30.1694    74.8432  -143.5521   461.8479   605.4000 
  4  17      4534     4534.0  Left-Hippocampus                   2.0828    23.2831  -113.9432   131.5358   245.4790

ces.abs-masked.bb.stats

# Title Segmentation Statistics 
# 
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
# cmdline mri_segstats --seg /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/aparc+aseg.mgz --ctab /home/nmrclass/freesurfer/FreeSurferColorLUT.txt --id 1021 --id 1022 --id 1030 --id 17 --i ces.anat.bb.mgh --sum ces.abs-masked.bb.stats --mask sig.anat.bb.mgh --maskthresh 2 --masksign abs 
# sysname  Linux
# hostname nmrclass33
# machine  x86_64
# user     nmrclass
# anatomy_type volume
# 
# SegVolFile /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/aparc+aseg.mgz 
# SegVolFileTimeStamp  2017/02/08 11:13:38 
# ColorTable /home/nmrclass/freesurfer/FreeSurferColorLUT.txt 
# ColorTableTimeStamp 2017/01/18 17:00:02 
# MaskVolFile  sig.anat.bb.mgh 
#   MaskVolFileTimeStamp  2018/02/21 13:09:26 
#   MaskThresh 2.000000 
#   MaskSign   abs 
#   MaskFrame  0 
#   MaskInvert 0 
# InVolFile  ces.anat.bb.mgh 
# InVolFileTimeStamp  2018/02/21 12:17:20 
# InVolFrame 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 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
# NRows 4 
# NTableCols 10 
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range  
  1 1021      1530     1530.0  ctx-lh-pericalcarine             182.5064   164.3479  -111.9001   713.9155   825.8157 
  2 1022      5935     5935.0  ctx-lh-postcentral                60.9178   100.7243  -232.6694   461.8479   694.5173 
  3 1030      5020     5020.0  ctx-lh-superiortemporal           89.1554   100.8434  -143.5521   461.8479   605.4000 
  4  17       136      136.0  Left-Hippocampus                  24.2060    63.0450  -113.9432   131.5358   245.4790

ces.pos-masked.bb.stats

# Title Segmentation Statistics 
# 
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
# cmdline mri_segstats --seg /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/aparc+aseg.mgz --ctab /home/nmrclass/freesurfer/FreeSurferColorLUT.txt --id 1021 --id 1022 --id 1030 --id 17 --i ces.anat.bb.mgh --sum ces.pos-masked.bb.stats --mask sig.anat.bb.mgh --maskthresh 2 --masksign pos 
# sysname  Linux
# hostname nmrclass33
# machine  x86_64
# user     nmrclass
# anatomy_type volume
# 
# SegVolFile /home/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/aparc+aseg.mgz 
# SegVolFileTimeStamp  2017/02/08 11:13:38 
# ColorTable /home/nmrclass/freesurfer/FreeSurferColorLUT.txt 
# ColorTableTimeStamp 2017/01/18 17:00:02 
# MaskVolFile  sig.anat.bb.mgh 
#   MaskVolFileTimeStamp  2018/02/21 13:13:42 
#   MaskThresh 2.000000 
#   MaskSign   pos 
#   MaskFrame  0 
#   MaskInvert 0 
# InVolFile  ces.anat.bb.mgh 
# InVolFileTimeStamp  2018/02/21 12:17:20 
# InVolFrame 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 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
# NRows 4 
# NTableCols 10 
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range  
  1 1021      1422     1422.0  ctx-lh-pericalcarine             200.5127   156.3413    32.1526   713.9155   681.7629 
  2 1022      4340     4340.0  ctx-lh-postcentral               107.5646    72.6399    19.5321   461.8479   442.3158 
  3 1030      4300     4300.0  ctx-lh-superiortemporal          112.4998    89.1221    25.4251   461.8479   436.4228 
  4  17        77       77.0  Left-Hippocampus                  75.2143    28.8035    43.2457   131.5358    88.2900

ces.pos-masked.vol.stats

Measure:volume  ctx-lh-pericalcarine    ctx-lh-postcentral      ctx-lh-superiortemporal Left-Hippocampus
0       1424.0  4339.0  4283.0  79.0
1       1246.0  4780.0  4049.0  186.0
2       609.0   4057.0  2990.0  121.0
3       843.0   2928.0  2236.0  146.0
4       1614.0  4003.0  3873.0  232.0

ces.abs-masked.mean.stats

Measure:mean    ctx-lh-pericalcarine    ctx-lh-postcentral      ctx-lh-superiortemporal Left-Hippocampus
0       180.1391        60.8179 88.2699 26.6048
1       162.6065        70.9748 78.5134 -1.1652
2       264.1356        38.3964 73.2994 -42.7581
3       182.7722        74.2692 97.7955 31.554
4       118.7494        57.6731 96.149  10.9517

ces.pos-masked.mean.stats

Measure:mean    ctx-lh-pericalcarine    ctx-lh-postcentral      ctx-lh-superiortemporal Left-Hippocampus
0       198.5072        107.5108  111.8215      75.6666
1       232.2992        108.0577  121.9527      37.9277
2       336.5665        111.2593  136.4619      81.3814
3       196.1099        81.4932   127.5857      77.9514
4       120.5139        91.797    113.7618      39.2072

MultiModalTutorialV6.0/BBStats (last edited 2018-02-21 15:01:58 by BramDiamond)