lh.aparc.stats


# Table of FreeSurfer cortical parcellation anatomical statistics 
# 
# CreationTime 2020/07/16-07:48:15-GMT
# generating_program mris_anatomical_stats
# cvs_version 7.1.0
# mrisurf.c-cvs_version 7.1.0
# 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 afni_t2 lh white 
# sysname  Darwin
# hostname macpro.local
# machine  x86_64
# user     taeylee
# 
# SUBJECTS_DIR /Users/taeylee/desktop/subjects
# anatomy_type surface
# subjectname afni_t2
# hemi lh
# AnnotationFile ../label/lh.aparc.annot
# AnnotationFileTimeStamp 2020/07/16 16:08:38
# Measure Cortex, NumVert, Number of Vertices, 114677, unitless
# Measure Cortex, WhiteSurfArea, White Surface Total Area, 78667.6, mm^2
# Measure Cortex, MeanThickness, Mean Thickness, 2.4237, mm
# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3
# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1038313.000000, mm^3
# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1013412.000000, mm^3
# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1013412.000000, mm^3
# Measure Cortex, CortexVol, Total cortical gray matter volume, 436041.342420, mm^3
# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 910971.000000, mm^3
# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 886070.000000, mm^3
# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1501571.972164, 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                                 1532   1024   2506  2.623 0.401     0.098     0.020        7     1.3
caudalanteriorcingulate                   838    556   1513  2.419 0.686     0.107     0.019        7     0.7
caudalmiddlefrontal                      3151   2130   5947  2.458 0.550     0.119     0.028       26     3.6
cuneus                                   2172   1462   2809  1.807 0.470     0.134     0.036       28     3.0
entorhinal                                662    478   1943  2.903 0.740     0.145     0.052       10     1.3
fusiform                                 3508   2484   7274  2.528 0.615     0.136     0.037       49     5.0
inferiorparietal                         6753   4588  12789  2.446 0.537     0.117     0.025       71     6.7
inferiortemporal                         4240   3149  11033  2.767 0.774     0.143     0.040       64     6.8
isthmuscingulate                         1336    924   2628  2.466 0.739     0.124     0.033       16     1.6
lateraloccipital                         6857   4536  10156  2.075 0.596     0.138     0.034       87     9.3
lateralorbitofrontal                     3459   2539   7355  2.586 0.618     0.142     0.042       49     6.1
lingual                                  4302   3070   7086  2.084 0.625     0.142     0.038       54     6.6
medialorbitofrontal                      2490   1774   4671  2.333 0.628     0.128     0.036       31     3.5
middletemporal                           3891   2796   9842  2.737 0.678     0.127     0.035       45     5.3
parahippocampal                           916    593   2016  2.727 0.815     0.097     0.035        9     0.9
paracentral                              2286   1461   3674  2.302 0.623     0.110     0.029       17     2.7
parsopercularis                          1803   1296   3914  2.567 0.524     0.123     0.030       20     2.0
parsorbitalis                            1018    722   2627  2.714 0.633     0.134     0.033       13     1.3
parstriangularis                         1762   1247   3743  2.436 0.639     0.127     0.030       18     2.3
pericalcarine                            1914   1310   2111  1.740 0.469     0.137     0.040       24     2.9
postcentral                              5504   3518   7650  1.942 0.586     0.105     0.028       48     5.7
posteriorcingulate                       1595   1103   2946  2.321 0.701     0.126     0.029       18     2.0
precentral                               7201   4675  12697  2.527 0.606     0.123     0.036       65    10.5
precuneus                                5245   3651   9060  2.267 0.562     0.125     0.030       56     6.3
rostralanteriorcingulate                  891    617   2199  2.872 0.893     0.122     0.033       11     1.1
rostralmiddlefrontal                     6969   5031  14128  2.373 0.613     0.133     0.034       87     9.9
superiorfrontal                          9456   6517  19704  2.625 0.588     0.121     0.031       86    11.6
superiorparietal                         7932   5211  13198  2.192 0.581     0.119     0.027       79     8.4
superiortemporal                         5259   3507  10895  2.678 0.605     0.102     0.023       41     4.8
supramarginal                            4892   3380   9627  2.584 0.500     0.127     0.029       55     5.8
frontalpole                               389    313   1195  2.568 0.648     0.167     0.045        8     0.9
temporalpole                              749    516   1929  2.802 0.813     0.138     0.050        9     1.4
transversetemporal                        579    374    978  2.614 0.482     0.114     0.029        5     0.6
insula                                   3126   2117   6568  3.009 0.818     0.123     0.041       32     4.8

aseg.stats


# Title Segmentation Statistics 
# 
# generating_program mri_segstats
# cvs_version 7.1.0
# 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 /Applications/freesurfer/7.1.0/ASegStatsLUT.txt --subject afni_t2 
# sysname  Darwin
# hostname macpro.local
# machine  x86_64
# user     taeylee
# anatomy_type volume
# 
# SUBJECTS_DIR /Users/taeylee/desktop/subjects
# subjectname afni_t2
# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3
# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1038313.000000, mm^3
# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1013412.000000, mm^3
# Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 20707.000000, mm^3
# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 218504.194317, mm^3
# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 217537.148103, mm^3
# Measure Cortex, CortexVol, Total cortical gray matter volume, 436041.342420, mm^3
# Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 200979.000000, mm^3
# Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 198637.000000, mm^3
# Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 399616.000000, mm^3
# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 51562.000000, mm^3
# Measure TotalGray, TotalGrayVol, Total gray matter volume, 593046.342420, mm^3
# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 910971.000000, mm^3
# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 886070.000000, mm^3
# Measure Mask, MaskVol, Mask Volume, 1529172.000000, mm^3
# Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 0.691484, unitless
# Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 1.018381, 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, 26, unitless
# Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 50, unitless
# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1501571.972164, mm^3
# SegVolFile mri/aseg.mgz 
# SegVolFileTimeStamp  2020/07/16 16:36:14 
# ColorTable /Applications/freesurfer/7.1.0/ASegStatsLUT.txt 
# ColorTableTimeStamp 2020/05/12 01:34:25 
# InVolFile  mri/norm.mgz 
# InVolFileTimeStamp  2020/07/16 12:18:48 
# InVolFrame 0 
# PVVolFile  mri/norm.mgz 
# PVVolFileTimeStamp  2020/07/16 12:18:48 
# 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      9971    10260.8  Left-Lateral-Ventricle            29.7125    11.7771     9.0000    80.0000    71.0000 
  2   5       163      211.1  Left-Inf-Lat-Vent                 49.3620    11.1609    18.0000    77.0000    59.0000 
  3   7     10530    11312.3  Left-Cerebellum-White-Matter      89.3004     6.6013    28.0000   109.0000    81.0000 
  4   8     52936    52654.4  Left-Cerebellum-Cortex            70.1416    10.6957    15.0000    99.0000    84.0000 
  5  10      7312     7056.6  Left-Thalamus                     82.6255     9.2861    39.0000   103.0000    64.0000 
  6  11      3275     3252.9  Left-Caudate                      76.6815     8.4754    34.0000    99.0000    65.0000 
  7  12      4480     4444.7  Left-Putamen                      84.3464     5.9073    52.0000   102.0000    50.0000 
  8  13      1534     1527.9  Left-Pallidum                     95.4589     4.4926    69.0000   120.0000    51.0000 
  9  14       985     1025.1  3rd-Ventricle                     35.8030    12.8513    13.0000    76.0000    63.0000 
 10  15      2082     2219.3  4th-Ventricle                     33.2440    11.0577     8.0000    71.0000    63.0000 
 11  16     17627    17369.1  Brain-Stem                        82.0423    10.6772    21.0000   109.0000    88.0000 
 12  17      3944     3826.0  Left-Hippocampus                  69.4341     7.6920    29.0000    95.0000    66.0000 
 13  18      1515     1463.7  Left-Amygdala                     73.9710     7.4599    42.0000    95.0000    53.0000 
 14  24      1127     1113.6  CSF                               44.2875    11.7413    16.0000    82.0000    66.0000 
 15  26       453      446.0  Left-Accumbens-area               72.9095     4.9976    49.0000    88.0000    39.0000 
 16  28      3573     3441.1  Left-VentralDC                    87.6325    10.3539    38.0000   114.0000    76.0000 
 17  30        17       32.3  Left-vessel                       56.4118     5.8743    44.0000    67.0000    23.0000 
 18  31       752      693.3  Left-choroid-plexus               47.8205    10.5267    19.0000    78.0000    59.0000 
 19  43      8874     8971.2  Right-Lateral-Ventricle           30.6520    12.4962     2.0000    92.0000    90.0000 
 20  44       183      235.9  Right-Inf-Lat-Vent                55.7377    12.2491    22.0000   103.0000    81.0000 
 21  46     11369    11711.2  Right-Cerebellum-White-Matter     88.5666     7.5417    34.0000   109.0000    75.0000 
 22  47     52507    52578.5  Right-Cerebellum-Cortex           72.6274    11.0136    15.0000   108.0000    93.0000 
 23  49      6689     6364.3  Right-Thalamus                    82.7834     9.7361    29.0000   102.0000    73.0000 
 24  50      3445     3377.9  Right-Caudate                     76.8035     7.9319    40.0000   103.0000    63.0000 
 25  51      4329     4374.2  Right-Putamen                     86.8616     6.3656    43.0000   103.0000    60.0000 
 26  52      1670     1651.1  Right-Pallidum                    98.2796     4.7631    60.0000   112.0000    52.0000 
 27  53      3654     3543.7  Right-Hippocampus                 70.7211     7.7353    22.0000   100.0000    78.0000 
 28  54      1585     1567.3  Right-Amygdala                    73.8808     6.9580    35.0000    95.0000    60.0000 
 29  58       482      452.0  Right-Accumbens-area              75.1805     5.6941    55.0000    95.0000    40.0000 
 30  60      3622     3400.3  Right-VentralDC                   88.7198    11.2893    29.0000   114.0000    85.0000 
 31  62         8       20.3  Right-vessel                      55.2500     8.3964    47.0000    71.0000    24.0000 
 32  63       764      750.2  Right-choroid-plexus              50.5458    10.0601    25.0000    76.0000    51.0000 
 33  72         0        0.0  5th-Ventricle                      0.0000     0.0000     0.0000     0.0000     0.0000 
 34  77       626      526.3  WM-hypointensities                69.2125    11.4939    43.0000   111.0000    68.0000 
 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        75       84.8  Optic-Chiasm                      67.1733    15.2061    22.0000    96.0000    74.0000 
 41 251      1001      922.3  CC_Posterior                      93.6434    15.0514    26.0000   116.0000    90.0000 
 42 252       651      557.0  CC_Mid_Posterior                  85.3564    19.2853    30.0000   113.0000    83.0000 
 43 253       512      463.9  CC_Central                        92.4980    16.5128    36.0000   114.0000    78.0000 
 44 254       624      588.6  CC_Mid_Anterior                   93.5176    13.9148    42.0000   116.0000    74.0000 
 45 255       856      846.8  CC_Anterior                       96.1647    10.8274    41.0000   112.0000    71.0000 

3dresample


  usage: 3dresample [options] -prefix OUT_DSET -input IN_DSET

  examples:

    3dresample -orient asl -rmode NN -prefix asl.dset -input in+orig
    3dresample -dxyz 1.0 1.0 0.9 -prefix 119.dset -input in+tlrc
    3dresample -master master+orig -prefix new.dset -input old+orig.  
    (resample을 한 이후 해당 파일을 master로 놓고 이후의 파일들을 맞추는 것이 좋다)

    -rmode RESAM     : use this resampling method
          e.g.  -rmode Linear
          default is NN (nearest neighbor)

          The resampling method string RESAM should come
          from the set {'NN', 'Li', 'Cu', 'Bk'}.  These
          are for 'Nearest Neighbor', 'Linear', 'Cubic'
          and 'Blocky' interpolation, respectively.

          For details, go to the 'Define Datamode' panel
          of the afni GUI, click BHelp and then the
          'ULay resam mode' menu.


taeylee@imac data % 3dinfo t1.nii
++ 3dinfo: AFNI version=AFNI_20.2.02 (Jul 12 2020) [64-bit]

Dataset File:    /Users/taeylee/Desktop/data/t1.nii
Identifier Code: AFN_fkRhSIgQ09f4pkYksNCTqA  Creation Date: Fri Jul 17 13:04:53 2020
Template Space:  ORIG
Dataset Type:    Anat Bucket (-abuc)
Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode:    NIFTI
Storage Space:   22,413,312 (22 million) bytes
Geometry String: "MATRIX(0,0,-1,78.70412,0.9375,0,0,-127.7536,0,-0.9375,0,95.7162):256,256,171"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Anterior-to-Posterior
  second (y) = Superior-to-Inferior
  third  (z) = Left-to-Right   [-orient ASL]
R-to-L extent:   -91.296 [R] -to-    78.704 [L] -step-     1.000 mm [171 voxels]
A-to-P extent:  -127.754 [A] -to-   111.309 [P] -step-     0.938 mm [256 voxels]
I-to-S extent:  -143.346 [I] -to-    95.716 [S] -step-     0.938 mm [256 voxels]
Number of values stored at each pixel = 1
  -- At sub-brick #0 '?' datum type is short:            0 to           326

----- HISTORY -----
[taeylee@imac.local: Fri Jul 17 13:04:53 2020] to3d -quit_on_err -prefix t1.nii -use_last_elem I1000000 I2000000 I3000000 ... I1700001 I1710000
[taeylee@imac.local: Sat Jul 18 21:40:19 2020] {AFNI_20.2.02:macos_10.12_local} 3drefit -deoblique t1.nii

taeylee@imac data % 3dresample -orient rai -dxyz 1.0 1.0 1.0 -prefix t1_al+orig -input t1.nii
taeylee@imac data % 3dinfo t1_al+orig 
++ 3dinfo: AFNI version=AFNI_20.2.02 (Jul 12 2020) [64-bit]

Dataset File:    t1_al+orig
Identifier Code: AFN_HxKLDpdL-4cjuC73j-TWmA  Creation Date: Sat Jul 18 21:59:08 2020
Template Space:  ORIG
Dataset Type:    Anat Bucket (-abuc)
Byte Order:      LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode:    BRIK
Storage Space:   19,699,200 (20 million) bytes
Geometry String: "MATRIX(1,0,0,-91.29588,0,1,0,-127.7224,0,0,1,-143.315):171,240,240"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Right-to-Left
  second (y) = Anterior-to-Posterior
  third  (z) = Inferior-to-Superior   [-orient RAI]
R-to-L extent:   -91.296 [R] -to-    78.704 [L] -step-     1.000 mm [171 voxels]
A-to-P extent:  -127.722 [A] -to-   111.278 [P] -step-     1.000 mm [240 voxels]
I-to-S extent:  -143.315 [I] -to-    95.685 [S] -step-     1.000 mm [240 voxels]
Number of values stored at each pixel = 1
  -- At sub-brick #0 '#0' datum type is short:            0 to           326

----- HISTORY -----
[taeylee@imac.local: Fri Jul 17 13:04:53 2020] to3d -quit_on_err -prefix t1.nii -use_last_elem I1000000 I2000000 I3000000 ... I1700001 I1710000
[taeylee@imac.local: Sat Jul 18 21:40:19 2020] {AFNI_20.2.02:macos_10.12_local} 3drefit -deoblique t1.nii
[taeylee@imac.local: Sat Jul 18 21:59:08 2020] {AFNI_20.2.02:macos_10.12_local} 3dresample -orient rai -dxyz 1.0 1.0 1.0 -prefix t1_al+orig -input t1.nii