Merge pull request #35 from nikhil153/gh-pages

added local data
carpentries-incubator · May 27, 2021 · ef33b03 · ef33b03
2 parents b4d1307 + bb5a2f4
commit ef33b03
Show file tree

Hide file tree

Showing 44 changed files with 2,250 additions and 68 deletions.
diff --git a/code/1_sMRI_modalities.ipynb b/code/1_sMRI_modalities.ipynb
diff --git a/code/2_sMRI_image_cleanup.ipynb b/code/2_sMRI_image_cleanup.ipynb
@@ -54,7 +54,6 @@
     "import nilearn\n",
     "from nilearn import datasets\n",
     "from nilearn import plotting\n",
-    "\n",
     "import os"
    ]
   },

diff --git a/index.md b/index.md
@@ -4,6 +4,8 @@ root: .  # Is the only page that doesn't follow the pattern /:path/index.html
 permalink: index.html  # Is the only page that doesn't follow the pattern /:path/index.html
 ---
 
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/carpentries-incubator/SDC-BIDS-sMRI/gh-pages)
+
 Welcome to the **Structural Neuroimaging Analysis in Python** workshop! 
 
 The primary goals of this workshop are:
@@ -16,19 +18,22 @@ Things to keep in mind:
 2. In structural neuroimaging, MR scans can refer to several different image modalities including, T1-weighted, T2-weighted, diffusion weighted images (DWI), proton-densty (PD), Fluid attenuation inversion recovery (FLAIR) etc. 
 3. MR (pre)processing pipeline is a set of sequential image processing tasks performed on acquired MR scans prior to the statistical analyese. 
 4. MR software packages: In order to standardize and simplify computational effort, several software packages encapsulate MR (pre)processing pipelines. Thus as a user, you need not know the details of each image processing algorithm. Nevertheless it is useful to understand the key objectives of these tasks, the corresponding computational approaches, and their impact on the downstream analyses. This will 1) help developers to improve the underlying algorithms and 2) help users to customize the neuorimaging pipelines according to specific dataset requirements. Here are a few common software packages: 
-    - FressSurfer
-    - FSL
-    - CIVET
-    - SPM (mostly for functional data)
-    - AFNI (mostly for functional data)
-    - sMRIprep/fMRIprep
+
+    - [FressSurfer](https://surfer.nmr.mgh.harvard.edu/)
+    - [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)
+    - [CIVET](http://www.bic.mni.mcgill.ca/ServicesSoftware/CIVET-2-1-0-Table-of-Contents)
+    - [ANTs](http://stnava.github.io/ANTs/)
+    - [SPM](https://www.fil.ion.ucl.ac.uk/spm/) (mostly for functional data)
+    - [AFNI](https://afni.nimh.nih.gov/) (mostly for functional data) 
+    - [sMRIprep](https://github.com/nipreps/smriprep) or [fMRIprep](https://github.com/nipreps/fmriprep) (pipeline customization)
 
 
 _Note: All of this may sound complicated, but we'll explain things step-by-step in depth with practical examples as the course goes along. We will begin our computational journey stating from how an MR image is acquired, followed by several pre-processing tasks, with the end goal of conducting a statistical analysis to investigate neuroanatomical differences between patients and healthy controls groups._
 
 ## You Are Here!
 ![course_flow](fig/index/Course_flow_0.png)
 
+
 <!-- this is an html comment -->
 
 {% comment %} This is a comment in Liquid {% endcomment %}

diff --git a/local_data/2_sMRI_cleanup/sub001/mri/T1.mgz b/local_data/2_sMRI_cleanup/sub001/mri/T1.mgz
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/aparc+aseg.mgz b/local_data/2_sMRI_cleanup/sub001/mri/aparc+aseg.mgz
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/aparc.DKTatlas+aseg.mgz b/local_data/2_sMRI_cleanup/sub001/mri/aparc.DKTatlas+aseg.mgz
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/aparc.a2009s+aseg.mgz b/local_data/2_sMRI_cleanup/sub001/mri/aparc.a2009s+aseg.mgz
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/aseg.auto.mgz b/local_data/2_sMRI_cleanup/sub001/mri/aseg.auto.mgz
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/aseg.auto_noCCseg.mgz b/local_data/2_sMRI_cleanup/sub001/mri/aseg.auto_noCCseg.mgz
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/aseg.mgz b/local_data/2_sMRI_cleanup/sub001/mri/aseg.mgz
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/brainmask.mgz b/local_data/2_sMRI_cleanup/sub001/mri/brainmask.mgz
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/nu.mgz b/local_data/2_sMRI_cleanup/sub001/mri/nu.mgz
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/orig.mgz b/local_data/2_sMRI_cleanup/sub001/mri/orig.mgz
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/transforms/cc_up.lta b/local_data/2_sMRI_cleanup/sub001/mri/transforms/cc_up.lta
@@ -0,0 +1,30 @@
+# transform file /home/nikhil/projects/neurodocker/nipype_tutorial/freesurfer/sub001/mri/transforms/cc_up.lta
+# created by nikhil on Tue Apr  6 15:19:41 2021
+
+type      = 0 # LINEAR_VOX_TO_VOX
+nxforms   = 1
+mean      = 129.0000 135.0000 129.0000
+sigma     = 10000.0000
+1 4 4
+9.974024295806885e-01 -4.251025244593620e-02 5.814732611179352e-02 -1.239935994148254e+00 
+4.243819415569305e-02 9.990959763526917e-01 2.474094275385141e-03 6.396048545837402e+00 
+-5.819993838667870e-02 0.000000000000000e+00 9.983048439025879e-01 6.610050201416016e+00 
+0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 
+src volume info
+valid = 1  # volume info valid
+filename = /home/nikhil/projects/neurodocker/nipype_tutorial/freesurfer/sub001/mri/norm.mgz
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00
+zras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+cras   = -8.583132171630859e+01 -9.457855224609375e-01 5.000000000000000e-01
+dst volume info
+valid = 1  # volume info valid
+filename = /home/nikhil/projects/neurodocker/nipype_tutorial/freesurfer/sub001/mri/norm.mgz
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00
+zras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+cras   = -8.583132171630859e+01 -9.457855224609375e-01 5.000000000000000e-01
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/transforms/talairach.auto.xfm b/local_data/2_sMRI_cleanup/sub001/mri/transforms/talairach.auto.xfm
@@ -0,0 +1,8 @@
+MNI Transform File
+% avi2talxfm
+
+Transform_Type = Linear;
+Linear_Transform = 
+1.053177 -0.061204 -0.060685 90.310684
+0.070210 1.009246 0.117766 -9.806847
+0.023069 -0.117785 1.186777 13.209366;
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/transforms/talairach.auto.xfm.lta b/local_data/2_sMRI_cleanup/sub001/mri/transforms/talairach.auto.xfm.lta
@@ -0,0 +1,29 @@
+type      = 1 # LINEAR_RAS_TO_RAS
+nxforms   = 1
+mean      = 0.0000 0.0000 0.0000
+sigma     = 1.0000
+1 4 4
+1.053176999092102e+00 -6.120400130748749e-02 -6.068500131368637e-02 9.031068420410156e+01 
+7.021000236272812e-02 1.009245991706848e+00 1.177660003304482e-01 -9.806846618652344e+00 
+2.306899987161160e-02 -1.177849993109703e-01 1.186776995658875e+00 1.320936584472656e+01 
+0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 
+src volume info
+valid = 1  # volume info valid
+filename = /home/nikhil/projects/neurodocker/nipype_tutorial/freesurfer/sub001/mri/orig_nu.mgz
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00
+zras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+cras   = -8.583132171630859e+01 -9.457855224609375e-01 5.000000000000000e-01
+dst volume info
+valid = 1  # volume info valid
+filename = /opt/freesurfer-6.0.0-min/average/mni305.cor.mgz
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00
+zras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+cras   = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+subject fsaverage
+fscale 0.100000
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/transforms/talairach.lta b/local_data/2_sMRI_cleanup/sub001/mri/transforms/talairach.lta
@@ -0,0 +1,30 @@
+# transform file transforms/talairach.lta
+# created by nikhil on Tue Apr  6 13:02:09 2021
+
+type      = 0 # LINEAR_VOX_TO_VOX
+nxforms   = 1
+mean      = 129.0000 135.0000 129.0000
+sigma     = 10000.0000
+1 4 4
+1.035310864448547e+00 -5.322968959808350e-02 6.893639266490936e-02 -7.738219261169434e+00 
+2.411704696714878e-02 1.148522019386292e+00 5.860143527388573e-02 -4.360515213012695e+01 
+-7.657878845930099e-02 -6.251266598701477e-02 9.747626781463623e-01 1.660344839096069e+00 
+0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 
+src volume info
+valid = 1  # volume info valid
+filename = nu.mgz
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00
+zras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+cras   = -8.583132171630859e+01 -9.457855224609375e-01 5.000000000000000e-01
+dst volume info
+valid = 1  # volume info valid
+filename = /opt/freesurfer-6.0.0-min/average/RB_all_2016-05-10.vc700.gca
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00
+zras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+cras   = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/transforms/talairach.xfm b/local_data/2_sMRI_cleanup/sub001/mri/transforms/talairach.xfm
@@ -0,0 +1,8 @@
+MNI Transform File
+% avi2talxfm
+
+Transform_Type = Linear;
+Linear_Transform = 
+1.053177 -0.061204 -0.060685 90.310684
+0.070210 1.009246 0.117766 -9.806847
+0.023069 -0.117785 1.186777 13.209366;
diff --git a/local_data/2_sMRI_cleanup/sub001/mri/transforms/talairach_with_skull.lta b/local_data/2_sMRI_cleanup/sub001/mri/transforms/talairach_with_skull.lta
@@ -0,0 +1,30 @@
+# transform file transforms/talairach_with_skull.lta
+# created by nikhil on Tue Apr  6 12:11:55 2021
+
+type      = 0 # LINEAR_VOX_TO_VOX
+nxforms   = 1
+mean      = 129.0000 157.0000 140.0000
+sigma     = 10000.0000
+1 4 4
+1.042325973510742e+00 -3.924698382616043e-02 4.048125073313713e-02 -7.795707702636719e+00 
+3.624658659100533e-02 1.252970337867737e+00 2.024739608168602e-02 -5.292900085449219e+01 
+-7.761660963296890e-02 1.142661087214947e-03 1.019986867904663e+00 -1.212160015106201e+01 
+0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 
+src volume info
+valid = 1  # volume info valid
+filename = nu.mgz
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00
+zras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+cras   = -8.583132171630859e+01 -9.457855224609375e-01 5.000000000000000e-01
+dst volume info
+valid = 1  # volume info valid
+filename = /opt/freesurfer-6.0.0-min/average/RB_all_withskull_2016-05-10.vc700.gca
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00
+zras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+cras   = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
diff --git a/local_data/2_sMRI_cleanup/sub001/stats/aseg.stats b/local_data/2_sMRI_cleanup/sub001/stats/aseg.stats
@@ -0,0 +1,125 @@
+# 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 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 /opt/freesurfer-6.0.0-min/ASegStatsLUT.txt --subject sub001 
+# sysname  Linux
+# hostname JBLAB-laptop1
+# machine  x86_64
+# user     nikhil
+# anatomy_type volume
+# 
+# SUBJECTS_DIR /home/nikhil/projects/neurodocker/nipype_tutorial/freesurfer
+# subjectname sub001
+# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1207330.000000, mm^3
+# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1181804.000000, mm^3
+# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1181996.028410, mm^3
+# Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 19789.000000, mm^3
+# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 263263.911286, mm^3
+# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 262440.156667, mm^3
+# Measure Cortex, CortexVol, Total cortical gray matter volume, 525704.067953, mm^3
+# Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 227017.706337, mm^3
+# Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 223831.254119, mm^3
+# Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 450848.960456, mm^3
+# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 63823.000000, mm^3
+# Measure TotalGray, TotalGrayVol, Total gray matter volume, 702689.067953, mm^3
+# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1062731.028410, mm^3
+# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1042942.028410, mm^3
+# Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 1040097.000000, mm^3
+# Measure Mask, MaskVol, Mask Volume, 1639795.000000, mm^3
+# Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 0.795071, unitless
+# Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 1.079865, unitless
+# Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 50, unitless
+# Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 30, unitless
+# Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 80, unitless
+# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1518517.873449, mm^3
+# SegVolFile mri/aseg.mgz 
+# SegVolFileTimeStamp  2021/04/06 19:55:39 
+# ColorTable /opt/freesurfer-6.0.0-min/ASegStatsLUT.txt 
+# ColorTableTimeStamp 2017/01/18 17:00:02 
+# InVolFile  mri/norm.mgz 
+# InVolFileTimeStamp  2021/04/06 13:03:03 
+# InVolFrame 0 
+# PVVolFile  mri/norm.mgz 
+# PVVolFileTimeStamp  2021/04/06 13:03:03 
+# 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      8771     9124.1  Left-Lateral-Ventricle            20.7584    13.9166     0.0000    84.0000    84.0000 
+  2   5       577      615.8  Left-Inf-Lat-Vent                 35.2998    15.9115     0.0000    83.0000    83.0000 
+  3   7     13929    14818.6  Left-Cerebellum-White-Matter      81.7133     8.4380    13.0000   106.0000    93.0000 
+  4   8     56122    56061.7  Left-Cerebellum-Cortex            52.5078    12.5745     0.0000   130.0000   130.0000 
+  5  10      8494     8188.1  Left-Thalamus-Proper              83.4987    10.3988    19.0000   109.0000    90.0000 
+  6  11      4309     4334.8  Left-Caudate                      71.5516     7.7897    38.0000    99.0000    61.0000 
+  7  12      5436     5418.0  Left-Putamen                      80.5486     6.3864    48.0000   106.0000    58.0000 
+  8  13      2156     2102.8  Left-Pallidum                     95.1633     5.3868    71.0000   111.0000    40.0000 
+  9  14      1137     1187.8  3rd-Ventricle                     28.6016    15.2157     2.0000    79.0000    77.0000 
+ 10  15      3587     3740.4  4th-Ventricle                     14.2138    10.1541     0.0000    65.0000    65.0000 
+ 11  16     20001    20132.3  Brain-Stem                        80.7432    10.5844    13.0000   125.0000   112.0000 
+ 12  17      4250     4074.2  Left-Hippocampus                  62.3169     9.2062    13.0000   108.0000    95.0000 
+ 13  18      1847     1784.3  Left-Amygdala                     64.3546     7.1456    31.0000    91.0000    60.0000 
+ 14  24      1013     1013.6  CSF                               33.8045    12.9771     6.0000    68.0000    62.0000 
+ 15  26       663      673.0  Left-Accumbens-area               69.0724     6.4822    29.0000    98.0000    69.0000 
+ 16  28      4428     4201.4  Left-VentralDC                    89.0976    12.4963    21.0000   109.0000    88.0000 
+ 17  30         4        8.6  Left-vessel                       56.0000     3.1623    52.0000    59.0000     7.0000 
+ 18  31       650      565.3  Left-choroid-plexus               45.2400    12.1988    19.0000    86.0000    67.0000 
+ 19  43      8683     8976.5  Right-Lateral-Ventricle           20.9663    13.9983     0.0000    85.0000    85.0000 
+ 20  44       361      393.1  Right-Inf-Lat-Vent                32.0443    17.2848     0.0000    76.0000    76.0000 
+ 21  46     14510    15185.5  Right-Cerebellum-White-Matter     77.3130     8.1816     8.0000   112.0000   104.0000 
+ 22  47     55878    56003.1  Right-Cerebellum-Cortex           49.9057    12.6932     0.0000    95.0000    95.0000 
+ 23  49      8623     8275.7  Right-Thalamus-Proper             83.1272    10.1998    15.0000   108.0000    93.0000 
+ 24  50      4679     4595.0  Right-Caudate                     71.8949     8.5059    31.0000    98.0000    67.0000 
+ 25  51      5625     5572.3  Right-Putamen                     78.5858     7.1141    28.0000   103.0000    75.0000 
+ 26  52      1922     1824.4  Right-Pallidum                    92.4246     5.8170    31.0000   110.0000    79.0000 
+ 27  53      4454     4291.2  Right-Hippocampus                 61.7443     9.0039    16.0000   100.0000    84.0000 
+ 28  54      1777     1715.3  Right-Amygdala                    60.3742     7.5962    33.0000    92.0000    59.0000 
+ 29  58       756      746.3  Right-Accumbens-area              67.1958     6.0817    47.0000    93.0000    46.0000 
+ 30  60      4451     4264.5  Right-VentralDC                   88.6989    12.8147    15.0000   109.0000    94.0000 
+ 31  62        15       21.5  Right-vessel                      54.2000     6.9096    40.0000    66.0000    26.0000 
+ 32  63       777      669.3  Right-choroid-plexus              44.2085    13.8733    14.0000    79.0000    65.0000 
+ 33  72         0        0.0  5th-Ventricle                      0.0000     0.0000     0.0000     0.0000     0.0000 
+ 34  77      1449     1312.0  WM-hypointensities                64.5162    16.2334     0.0000    98.0000    98.0000 
+ 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       112      101.3  Optic-Chiasm                      75.9554    20.3958    24.0000   110.0000    86.0000 
+ 41 251       831      781.5  CC_Posterior                      98.9519    13.9526    40.0000   111.0000    71.0000 
+ 42 252       504      454.9  CC_Mid_Posterior                  91.1131    16.7744    23.0000   109.0000    86.0000 
+ 43 253       634      555.5  CC_Central                        89.1435    17.9143    33.0000   113.0000    80.0000 
+ 44 254       483      433.6  CC_Mid_Anterior                   95.0932    17.3683    24.0000   116.0000    92.0000 
+ 45 255      1106     1038.9  CC_Anterior                      100.6347    18.6827    31.0000   124.0000    93.0000