SlideShare une entreprise Scribd logo
1  sur  80
Télécharger pour lire hors ligne
Slicer Tutorial 6  Module: vtkFreeSurferReaders  Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.
Acknowledgments ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Disclaimer ,[object Object],[object Object],[object Object],[object Object]
Materials Needed ,[object Object],[object Object],[object Object],[object Object]
Goal of this tutorial Guide you step-by-step through the process of  loading and viewing FreeSurfer segmentation, surface reconstruction and parcellation results  within Slicer.
Prerequisites ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],https://surfer.nmr.mgh.harvard.edu/fswiki https://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsTutorial/
Prerequisites ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],http://www.namic.org/Wiki/index.php/ Slicer:Workshops:User_Training_101
vtkFreeSurferReaders Module
Loading FreeSurfer Data ,[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],Overview of Training 6
vtkFreeSurferReaders Module Select the Menu  Modules  in the  Main Panel Select the category  IO  and the   module  vtkFreeSurferReaders
vtkFreeSurferReaders Module The  vtkFreeSurferReaders  module appears in the  Main Panel  of Slicer. The  Volumes  tab comes up by default.
Loading a Brain file Brain.mgz Skull Stripping and Noise Filtering Watershed algorithm Intensity corrected  T1 volume FreeSurfer Pipeline
Loading a Brain file Select the Tab  Volumes  in the  FreeSurfer Module Click on  Browse  and select the subject  bert Click on the  mri  folder to access the brain volume.
Loading a Brain file Select the file  brain.mgz Select the data type  GrayScale Click  Apply
Loading a Brain file The volume  Brain.mgz  appears in the  Viewer .
Loading a Brain file Click on the  V  buttons in the  Axial, Sagittal  and  Coronal  views.
Loading a Brain file The three anatomical slices appear in the  3D Viewer .
Loading an ASEG  file Aseg.mgz Segmentation  Subcortical processing  Intensity corrected  T1 volume FreeSurfer Pipeline
Loading an ASEG file Select the Tab  Volumes  in the  FreeSurfer Module. Click on  Browse  and select the subject  bert Click on the  mri  folder to access the aseg volume.
Loading an ASEG file Select the file  aseg.mgz Select the data type  Label Map Click on  Apply
Loading an ASEG file The labels are superimposed on the gray level brain images. The volume  aseg.mgz  appears in the  Viewer .
Determining label numbers in an ASEG file # ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range 1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 2 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000 146.0000 3 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.0000 4 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.0000 5 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.0000 6 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 7 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.0000 8 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.0000 9 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.0000 10 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.0000 11 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.0000 12 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.0000 13 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.0000 14 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.0000 15 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.0000 16 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.0000 17 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.0000 18 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.0000 19 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.0000 20 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.0000 21 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.0000 22 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.0000 23 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.0000 24 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.0000 25 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.0000 26 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.0000 27 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.0000 28 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.0000 29 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.0000 30 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000 The file  aseg.stats  gives the list of the available segmented structures in the dataset. Example of the first 30 structures .
Determining label numbers in an ASEG file # ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range 1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 2 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000 146.0000 3 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.0000 4 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.0000 5 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.0000 6 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 7 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.0000 8 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.0000 9 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.0000 10 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.0000 11 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.0000 12 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.0000 13 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.0000 14 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.0000 15 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.0000 16 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.0000 17 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.0000 18 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.0000 19 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.0000 20 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.0000 21 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.0000 22 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.0000 23 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.0000 24 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.0000 25 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.0000 26 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.0000 27 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.0000 28 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.0000 29 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.0000 30 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000 The label #10 represents the  Left-Thalamus Proper. The corresponding segmented volume is available in the current dataset.
Determining label numbers in an ASEG file # ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range 1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 2 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000 146.0000 3 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.0000 4 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.0000 5 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.0000 6 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 7 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.0000 8 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.0000 9 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.0000 10 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.0000 11 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.0000 12 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.0000 13 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.0000 14 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.0000 15 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.0000 16 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.0000 17 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.0000 18 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.0000 19 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.0000 20 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.0000 21 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.0000 22 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.0000 23 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.0000 24 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.0000 25 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.0000 26 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.0000 27 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.0000 28 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.0000 29 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.0000 30 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000 The label #19 representing the  Left-Insula. The corresponding segmented volume is not available in the current dataset.
[object Object],[object Object],[object Object],[object Object],[object Object],Overview of Training 6
Overlay Brain and Segmentation Click on the button  Bg (Background)  and   select the volume  aseg  in the  Axial  view.
Overlay Brain and Segmentation Move the mouse over   the labels in the  Axial  view.
Overlay Brain and Segmentation The names of the labels appear in the window.
Overlay Brain and Segmentation Find the labels corresponding to the  Left Thalamus Proper ,  Left Caudate  and  Left Putamen  in the three anatomical views.
Overlay Brain and Segmentation Left Thalamus Proper = 10
Overlay Brain and Segmentation Left Putamen = 12
Overlay Brain and Segmentation Left Caudate = 11
Overlay Brain and Segmentation Select  View  3D  in the  MainMenu
Overlay Brain and Segmentation Drag right mouse button  down  in the 3D Viewer to  zoom in .
Overlay Brain and Segmentation The Viewer displays a zoom view of the  brain  and  aseg  slices superimposed.   Drag right mouse button  up  in the  Viewer to  zoom out .
[object Object],[object Object],[object Object],[object Object],[object Object],Overview of Training 6
Building a single Model Select the module  ModelMaker  in the  MainMenu   Select the panel  Create Select the Volume  aseg  and click on the button  Label
Building a single Model Slicer displays the  Color Map  corresponding to the structures that  FreeSurfer  can segment.
Building a single Model Move the mouse over the table and select the label of the  right hippocampus  (label 53).
Building a single Model The label of the  right hippocampus  appears in the  Create  panel. Click on  Create  to build the 3D model.
Building a single Model The 3D model of the right  hippocampus  appears in the  Viewer.  Switch to the view  3D ,   and drag right mouse button down in the  Viewer  to zoom in.
Building a single Model Slicer displays a zoom view of the right  hippocampus .
Building 3D Models Select the module  ModelMaker  in the  MainMenu   Select the panel  Create Multiple
Building 3D Models Select the  Volume   aseg  and click on the button  Starting Label The Panel  Create Multiple  provides the interface to build a set of continuous models from the values in the interval [Starting Label, Ending Label]
Building 3D Models Click on the label corresponding to the  Left Thalamus Proper  (Label 10).
Building 3D Models Click on the button  Ending Label The value and the color of the selected label appear in the panel.
Building 3D Models Click on the label corresponding to the  Left Pallidum  (Label 13).
Building 3D Models Click on  Create all  to build the 3D models of the selected labels. Slicer reconstructs the 3D models from the labels 10,11,12 and 13.
Building 3D Models The 3D models of the selected structures appear inside the  Viewer.
Building 3D Models Left click and move the mouse to orient the models in the  Viewer
Building 3D Models Click in the module  Models  in the  Main Menu  and select the panel  Display. The list of models appears in the panel. Deselect the models of the  Left Putamen  and  Left Caudate.
Building 3D Models Slicer displays the left   Thalamus Proper ,  left  Pallidum   and right   Hippocampus   in the  Viewer.
Building 3D Models Click on  Show None  to make all the models disappear from the Scene.
[object Object],[object Object],[object Object],[object Object],[object Object],Overview of Training 6
Loading Surfaces Select the panel  Models  in the  vtkFreeSurferReaders  module. Click on  Browse  and select the surface  lh.white  in the directory  subjects/bert/surf
Loading Surfaces Click  Apply  to load the surface in Slicer.  The name of the surface selected appears in the  Models  panel.
Loading Surface The surface of the white matter of the left hemisphere appears in the Viewer.
Parcellation Visualization In the panel  Models  click on  aparc  to select the parcellation map of the model  lh.white Click on  Apply  to load the overlay.
Parcellation Visualization Slicer displays the parcellation results overlaid on the white matter surface in the  Viewer.  Switch to  3D view  in the main menu and zoom in the model.
Parcellation Visualization Cortical parcellation of the white matter surface in the left hemisphere.
[object Object],[object Object],[object Object],[object Object],[object Object],Overview of Training 6
Group Statistics ,[object Object],[object Object],[object Object],[object Object]
Group Statistics Statistical Parametric Map Average Subject creation General Linear Modeling
Group Statistics - example Statistical Parametric Map sigt_Age_dossthickness-100lh.w Average Subject creation lh.pial_avg  For my cohort of x sujects, does cortical thickness vary with age?  General Linear Modeling  y_doss_thickness-100lh.fsgd
Group Statistics Select the Tab  Models  in the  vtkFreeSurferReaders  module. Click on  Browse  and select the surface  lh.pial_avg  in the directory  subjects/average/surf
Group Statistics Select the Tab  Display  in the  vtkFreeSurferReaders  module. Click on  Browse  and select the overlay  subjects/stats/sigt_Age_doss-thickness-100lh.w  Click on  Load Scalar File.
Group Statistics Slicer displays the statistical map as an overlay superimposed on the average surface. Move the model with the mouse to update the Viewer display.
Group Statistics Select the  Panel Plot  in the  vtkFreeSurferReaders  module. Click on  Browse  and select the file  y_doss-thickness-100lh.fsgd  in the directory  subjects/stats.
Group Statistics Select the  Active Model lh.pial_avg  in the list of models. Click on  Apply  to load the  Group Statistics  results.
Group Statistics Slicer displays  statistical distribution of  the  cortical thickness  of the left hemisphere   parameterized by the age of the population.
Group Statistics Select the  Mode  subject  in the Group Statistics Window.
Group Statistics Slicer displays the subjects included in the Statistical Analysis. Move the mouse over the subjects table and select the  subject #108.
Group Statistics A red circle shows the position of the subject #108 in the analysis.
Group Statistics The  Configure Classes  menu displays the visualization options of the population.
Group Statistics Select the pattern  diamond  and the color   black   for the male subjects. Select the pattern  circle   and the color  purple  for the female subjects.
Group Statistics Slicer updates the interface with the new configuration parameters.
Group Statistics To generate a plot for a particular vertex, select a point by clicking on the parametric map at that vertex on   the 3D model in the  Viewer
Group Statistics Slicer updates the thickness results with the values corresponding to the selected vertex.
Conclusion  ,[object Object],[object Object],[object Object],[object Object],[object Object]

Contenu connexe

Similaire à FreeSurfer Reader-3766

Kshivets iaslc toronto2018
Kshivets iaslc toronto2018Kshivets iaslc toronto2018
Kshivets iaslc toronto2018Oleg Kshivets
 
Spark Summit Dublin 2017 - MemSQL - Real-Time Image Recognition
Spark Summit Dublin 2017 - MemSQL - Real-Time Image RecognitionSpark Summit Dublin 2017 - MemSQL - Real-Time Image Recognition
Spark Summit Dublin 2017 - MemSQL - Real-Time Image RecognitionSingleStore
 
Bidm assignment airtrip data
Bidm assignment   airtrip dataBidm assignment   airtrip data
Bidm assignment airtrip dataSanmeet Dhokay
 
Prediction of Arterial Blood Gases(ABG) by Using Neural Network In Trauma Pat...
Prediction of Arterial Blood Gases(ABG) by Using Neural Network In Trauma Pat...Prediction of Arterial Blood Gases(ABG) by Using Neural Network In Trauma Pat...
Prediction of Arterial Blood Gases(ABG) by Using Neural Network In Trauma Pat...Mohammad Sabouri
 
realestate and MySQL devops melbourne
realestate and MySQL devops melbournerealestate and MySQL devops melbourne
realestate and MySQL devops melbournemysqldbahelp
 
kupdf.net_indian-steel-table.pdf
kupdf.net_indian-steel-table.pdfkupdf.net_indian-steel-table.pdf
kupdf.net_indian-steel-table.pdfParandh M
 
The Ciliate Species Names List Project
The Ciliate Species Names List ProjectThe Ciliate Species Names List Project
The Ciliate Species Names List Projectvibrantmanager
 
The OPC Data Logger Project
The OPC Data Logger ProjectThe OPC Data Logger Project
The OPC Data Logger ProjectKharel Thompson
 
Sheet1-242.7062237.1326187.084-242.7012236.922174.4266-244.3963224.docx
Sheet1-242.7062237.1326187.084-242.7012236.922174.4266-244.3963224.docxSheet1-242.7062237.1326187.084-242.7012236.922174.4266-244.3963224.docx
Sheet1-242.7062237.1326187.084-242.7012236.922174.4266-244.3963224.docxbjohn46
 
Prstat and Processes Oracle
Prstat and Processes OraclePrstat and Processes Oracle
Prstat and Processes OracleAnar Godjaev
 
slides36.pptx
slides36.pptxslides36.pptx
slides36.pptxDarSafwan
 
NEWSTAR LED's 600x600 48w led panel light 100lm per watt
NEWSTAR LED's 600x600 48w led panel light 100lm per wattNEWSTAR LED's 600x600 48w led panel light 100lm per watt
NEWSTAR LED's 600x600 48w led panel light 100lm per wattJason Gong
 
600x600mm 48w 6000k led panel lights
600x600mm 48w 6000k led panel lights600x600mm 48w 6000k led panel lights
600x600mm 48w 6000k led panel lightsJason Gong
 
IBM Global Security Kit as a Cryptographic layer for IBM middleware
IBM Global Security Kit as a Cryptographic layer for IBM middlewareIBM Global Security Kit as a Cryptographic layer for IBM middleware
IBM Global Security Kit as a Cryptographic layer for IBM middlewareOktawian Powazka
 
ABB POLIM-H..N High Voltage Surge Arresters AC up to 72 kV - AC Surge Arreste...
ABB POLIM-H..N High Voltage Surge Arresters AC up to 72 kV - AC Surge Arreste...ABB POLIM-H..N High Voltage Surge Arresters AC up to 72 kV - AC Surge Arreste...
ABB POLIM-H..N High Voltage Surge Arresters AC up to 72 kV - AC Surge Arreste...Thorne & Derrick International
 
ABB MWD High Voltage Surge Arresters AC 4kV - 44kV - AC Surge Arresters & Pr...
ABB MWD High Voltage Surge Arresters AC 4kV - 44kV -  AC Surge Arresters & Pr...ABB MWD High Voltage Surge Arresters AC 4kV - 44kV -  AC Surge Arresters & Pr...
ABB MWD High Voltage Surge Arresters AC 4kV - 44kV - AC Surge Arresters & Pr...Thorne & Derrick International
 

Similaire à FreeSurfer Reader-3766 (20)

Kshivets iaslc toronto2018
Kshivets iaslc toronto2018Kshivets iaslc toronto2018
Kshivets iaslc toronto2018
 
Spark Summit Dublin 2017 - MemSQL - Real-Time Image Recognition
Spark Summit Dublin 2017 - MemSQL - Real-Time Image RecognitionSpark Summit Dublin 2017 - MemSQL - Real-Time Image Recognition
Spark Summit Dublin 2017 - MemSQL - Real-Time Image Recognition
 
Bidm assignment airtrip data
Bidm assignment   airtrip dataBidm assignment   airtrip data
Bidm assignment airtrip data
 
Regression project
Regression projectRegression project
Regression project
 
Prediction of Arterial Blood Gases(ABG) by Using Neural Network In Trauma Pat...
Prediction of Arterial Blood Gases(ABG) by Using Neural Network In Trauma Pat...Prediction of Arterial Blood Gases(ABG) by Using Neural Network In Trauma Pat...
Prediction of Arterial Blood Gases(ABG) by Using Neural Network In Trauma Pat...
 
realestate and MySQL devops melbourne
realestate and MySQL devops melbournerealestate and MySQL devops melbourne
realestate and MySQL devops melbourne
 
kupdf.net_indian-steel-table.pdf
kupdf.net_indian-steel-table.pdfkupdf.net_indian-steel-table.pdf
kupdf.net_indian-steel-table.pdf
 
Aug2014 acrometrix
Aug2014 acrometrixAug2014 acrometrix
Aug2014 acrometrix
 
Annexure ii
Annexure iiAnnexure ii
Annexure ii
 
The Ciliate Species Names List Project
The Ciliate Species Names List ProjectThe Ciliate Species Names List Project
The Ciliate Species Names List Project
 
The OPC Data Logger Project
The OPC Data Logger ProjectThe OPC Data Logger Project
The OPC Data Logger Project
 
Sheet1-242.7062237.1326187.084-242.7012236.922174.4266-244.3963224.docx
Sheet1-242.7062237.1326187.084-242.7012236.922174.4266-244.3963224.docxSheet1-242.7062237.1326187.084-242.7012236.922174.4266-244.3963224.docx
Sheet1-242.7062237.1326187.084-242.7012236.922174.4266-244.3963224.docx
 
59 t 3-hig pressure
59 t 3-hig pressure59 t 3-hig pressure
59 t 3-hig pressure
 
Prstat and Processes Oracle
Prstat and Processes OraclePrstat and Processes Oracle
Prstat and Processes Oracle
 
slides36.pptx
slides36.pptxslides36.pptx
slides36.pptx
 
NEWSTAR LED's 600x600 48w led panel light 100lm per watt
NEWSTAR LED's 600x600 48w led panel light 100lm per wattNEWSTAR LED's 600x600 48w led panel light 100lm per watt
NEWSTAR LED's 600x600 48w led panel light 100lm per watt
 
600x600mm 48w 6000k led panel lights
600x600mm 48w 6000k led panel lights600x600mm 48w 6000k led panel lights
600x600mm 48w 6000k led panel lights
 
IBM Global Security Kit as a Cryptographic layer for IBM middleware
IBM Global Security Kit as a Cryptographic layer for IBM middlewareIBM Global Security Kit as a Cryptographic layer for IBM middleware
IBM Global Security Kit as a Cryptographic layer for IBM middleware
 
ABB POLIM-H..N High Voltage Surge Arresters AC up to 72 kV - AC Surge Arreste...
ABB POLIM-H..N High Voltage Surge Arresters AC up to 72 kV - AC Surge Arreste...ABB POLIM-H..N High Voltage Surge Arresters AC up to 72 kV - AC Surge Arreste...
ABB POLIM-H..N High Voltage Surge Arresters AC up to 72 kV - AC Surge Arreste...
 
ABB MWD High Voltage Surge Arresters AC 4kV - 44kV - AC Surge Arresters & Pr...
ABB MWD High Voltage Surge Arresters AC 4kV - 44kV -  AC Surge Arresters & Pr...ABB MWD High Voltage Surge Arresters AC 4kV - 44kV -  AC Surge Arresters & Pr...
ABB MWD High Voltage Surge Arresters AC 4kV - 44kV - AC Surge Arresters & Pr...
 

Plus de Kitware Kitware

Radial Thickness Calculation and Visualization for Volumetric Layers-8397
Radial Thickness Calculation and Visualization for Volumetric Layers-8397Radial Thickness Calculation and Visualization for Volumetric Layers-8397
Radial Thickness Calculation and Visualization for Volumetric Layers-8397Kitware Kitware
 
A Framework for Comparison and Evaluation of Nonlinear Intra-Subject Image Re...
A Framework for Comparison and Evaluation of Nonlinear Intra-Subject Image Re...A Framework for Comparison and Evaluation of Nonlinear Intra-Subject Image Re...
A Framework for Comparison and Evaluation of Nonlinear Intra-Subject Image Re...Kitware Kitware
 
Functional Magnetic Resonance Imaging Analysis-3765
Functional Magnetic Resonance Imaging Analysis-3765Functional Magnetic Resonance Imaging Analysis-3765
Functional Magnetic Resonance Imaging Analysis-3765Kitware Kitware
 
Diffusion Tensor Imaging Analysis-3749
Diffusion Tensor Imaging Analysis-3749Diffusion Tensor Imaging Analysis-3749
Diffusion Tensor Imaging Analysis-3749Kitware Kitware
 
Manual Segmentation-3747
Manual Segmentation-3747Manual Segmentation-3747
Manual Segmentation-3747Kitware Kitware
 
Data Loading and Visualization-3735
Data Loading and Visualization-3735Data Loading and Visualization-3735
Data Loading and Visualization-3735Kitware Kitware
 
Principles and Practices of Scientific Originology-8392
Principles and Practices of Scientific Originology-8392Principles and Practices of Scientific Originology-8392
Principles and Practices of Scientific Originology-8392Kitware Kitware
 
Principles and Practices of Scientific Originology-8391
Principles and Practices of Scientific Originology-8391Principles and Practices of Scientific Originology-8391
Principles and Practices of Scientific Originology-8391Kitware Kitware
 
ITK Tutorial Presentation Slides-953
ITK Tutorial Presentation Slides-953ITK Tutorial Presentation Slides-953
ITK Tutorial Presentation Slides-953Kitware Kitware
 
ITK Tutorial Presentation Slides-952
ITK Tutorial Presentation Slides-952ITK Tutorial Presentation Slides-952
ITK Tutorial Presentation Slides-952Kitware Kitware
 
ITK Tutorial Presentation Slides-951
ITK Tutorial Presentation Slides-951ITK Tutorial Presentation Slides-951
ITK Tutorial Presentation Slides-951Kitware Kitware
 
ITK Tutorial Presentation Slides-950
ITK Tutorial Presentation Slides-950ITK Tutorial Presentation Slides-950
ITK Tutorial Presentation Slides-950Kitware Kitware
 
ITK Tutorial Presentation Slides-949
ITK Tutorial Presentation Slides-949ITK Tutorial Presentation Slides-949
ITK Tutorial Presentation Slides-949Kitware Kitware
 
ITK Tutorial Presentation Slides-948
ITK Tutorial Presentation Slides-948ITK Tutorial Presentation Slides-948
ITK Tutorial Presentation Slides-948Kitware Kitware
 
ITK Tutorial Presentation Slides-947
ITK Tutorial Presentation Slides-947ITK Tutorial Presentation Slides-947
ITK Tutorial Presentation Slides-947Kitware Kitware
 
ITK Tutorial Presentation Slides-946
ITK Tutorial Presentation Slides-946ITK Tutorial Presentation Slides-946
ITK Tutorial Presentation Slides-946Kitware Kitware
 
ITK Tutorial Presentation Slides-945
ITK Tutorial Presentation Slides-945ITK Tutorial Presentation Slides-945
ITK Tutorial Presentation Slides-945Kitware Kitware
 
ITK Tutorial Presentation Slides-944
ITK Tutorial Presentation Slides-944ITK Tutorial Presentation Slides-944
ITK Tutorial Presentation Slides-944Kitware Kitware
 
ITK Tutorial Presentation Slides-943
ITK Tutorial Presentation Slides-943ITK Tutorial Presentation Slides-943
ITK Tutorial Presentation Slides-943Kitware Kitware
 
A Quantitative DTI Fiber Tract Analysis Suite-898
A Quantitative DTI Fiber Tract Analysis Suite-898A Quantitative DTI Fiber Tract Analysis Suite-898
A Quantitative DTI Fiber Tract Analysis Suite-898Kitware Kitware
 

Plus de Kitware Kitware (20)

Radial Thickness Calculation and Visualization for Volumetric Layers-8397
Radial Thickness Calculation and Visualization for Volumetric Layers-8397Radial Thickness Calculation and Visualization for Volumetric Layers-8397
Radial Thickness Calculation and Visualization for Volumetric Layers-8397
 
A Framework for Comparison and Evaluation of Nonlinear Intra-Subject Image Re...
A Framework for Comparison and Evaluation of Nonlinear Intra-Subject Image Re...A Framework for Comparison and Evaluation of Nonlinear Intra-Subject Image Re...
A Framework for Comparison and Evaluation of Nonlinear Intra-Subject Image Re...
 
Functional Magnetic Resonance Imaging Analysis-3765
Functional Magnetic Resonance Imaging Analysis-3765Functional Magnetic Resonance Imaging Analysis-3765
Functional Magnetic Resonance Imaging Analysis-3765
 
Diffusion Tensor Imaging Analysis-3749
Diffusion Tensor Imaging Analysis-3749Diffusion Tensor Imaging Analysis-3749
Diffusion Tensor Imaging Analysis-3749
 
Manual Segmentation-3747
Manual Segmentation-3747Manual Segmentation-3747
Manual Segmentation-3747
 
Data Loading and Visualization-3735
Data Loading and Visualization-3735Data Loading and Visualization-3735
Data Loading and Visualization-3735
 
Principles and Practices of Scientific Originology-8392
Principles and Practices of Scientific Originology-8392Principles and Practices of Scientific Originology-8392
Principles and Practices of Scientific Originology-8392
 
Principles and Practices of Scientific Originology-8391
Principles and Practices of Scientific Originology-8391Principles and Practices of Scientific Originology-8391
Principles and Practices of Scientific Originology-8391
 
ITK Tutorial Presentation Slides-953
ITK Tutorial Presentation Slides-953ITK Tutorial Presentation Slides-953
ITK Tutorial Presentation Slides-953
 
ITK Tutorial Presentation Slides-952
ITK Tutorial Presentation Slides-952ITK Tutorial Presentation Slides-952
ITK Tutorial Presentation Slides-952
 
ITK Tutorial Presentation Slides-951
ITK Tutorial Presentation Slides-951ITK Tutorial Presentation Slides-951
ITK Tutorial Presentation Slides-951
 
ITK Tutorial Presentation Slides-950
ITK Tutorial Presentation Slides-950ITK Tutorial Presentation Slides-950
ITK Tutorial Presentation Slides-950
 
ITK Tutorial Presentation Slides-949
ITK Tutorial Presentation Slides-949ITK Tutorial Presentation Slides-949
ITK Tutorial Presentation Slides-949
 
ITK Tutorial Presentation Slides-948
ITK Tutorial Presentation Slides-948ITK Tutorial Presentation Slides-948
ITK Tutorial Presentation Slides-948
 
ITK Tutorial Presentation Slides-947
ITK Tutorial Presentation Slides-947ITK Tutorial Presentation Slides-947
ITK Tutorial Presentation Slides-947
 
ITK Tutorial Presentation Slides-946
ITK Tutorial Presentation Slides-946ITK Tutorial Presentation Slides-946
ITK Tutorial Presentation Slides-946
 
ITK Tutorial Presentation Slides-945
ITK Tutorial Presentation Slides-945ITK Tutorial Presentation Slides-945
ITK Tutorial Presentation Slides-945
 
ITK Tutorial Presentation Slides-944
ITK Tutorial Presentation Slides-944ITK Tutorial Presentation Slides-944
ITK Tutorial Presentation Slides-944
 
ITK Tutorial Presentation Slides-943
ITK Tutorial Presentation Slides-943ITK Tutorial Presentation Slides-943
ITK Tutorial Presentation Slides-943
 
A Quantitative DTI Fiber Tract Analysis Suite-898
A Quantitative DTI Fiber Tract Analysis Suite-898A Quantitative DTI Fiber Tract Analysis Suite-898
A Quantitative DTI Fiber Tract Analysis Suite-898
 

Dernier

How to cure cirrhosis and chronic hepatitis naturally
How to cure cirrhosis and chronic hepatitis naturallyHow to cure cirrhosis and chronic hepatitis naturally
How to cure cirrhosis and chronic hepatitis naturallyZurück zum Ursprung
 
FDMA FLAP - The first dorsal metacarpal artery (FDMA) flap is used mainly for...
FDMA FLAP - The first dorsal metacarpal artery (FDMA) flap is used mainly for...FDMA FLAP - The first dorsal metacarpal artery (FDMA) flap is used mainly for...
FDMA FLAP - The first dorsal metacarpal artery (FDMA) flap is used mainly for...Shubhanshu Gaurav
 
EXERCISE PERFORMANCE.pptx, Lung function
EXERCISE PERFORMANCE.pptx, Lung functionEXERCISE PERFORMANCE.pptx, Lung function
EXERCISE PERFORMANCE.pptx, Lung functionkrishnareddy157915
 
Physiology of Smooth Muscles -Mechanics of contraction and relaxation
Physiology of Smooth Muscles -Mechanics of contraction and relaxationPhysiology of Smooth Muscles -Mechanics of contraction and relaxation
Physiology of Smooth Muscles -Mechanics of contraction and relaxationMedicoseAcademics
 
Trustworthiness of AI based predictions Aachen 2024
Trustworthiness of AI based predictions Aachen 2024Trustworthiness of AI based predictions Aachen 2024
Trustworthiness of AI based predictions Aachen 2024EwoutSteyerberg1
 
Red Blood Cells_anemia & polycythemia.pdf
Red Blood Cells_anemia & polycythemia.pdfRed Blood Cells_anemia & polycythemia.pdf
Red Blood Cells_anemia & polycythemia.pdfMedicoseAcademics
 
SGK LEUKEMIA KINH DÒNG BẠCH CÂU HẠT HAY.pdf
SGK LEUKEMIA KINH DÒNG BẠCH CÂU HẠT HAY.pdfSGK LEUKEMIA KINH DÒNG BẠCH CÂU HẠT HAY.pdf
SGK LEUKEMIA KINH DÒNG BẠCH CÂU HẠT HAY.pdfHongBiThi1
 
Bulimia nervosa ( Eating Disorders) Mental Health Nursing.
Bulimia nervosa ( Eating Disorders) Mental Health Nursing.Bulimia nervosa ( Eating Disorders) Mental Health Nursing.
Bulimia nervosa ( Eating Disorders) Mental Health Nursing.aarjukhadka22
 
ORAL HYPOGLYCAEMIC AGENTS - PART 2.pptx
ORAL HYPOGLYCAEMIC AGENTS  - PART 2.pptxORAL HYPOGLYCAEMIC AGENTS  - PART 2.pptx
ORAL HYPOGLYCAEMIC AGENTS - PART 2.pptxNIKITA BHUTE
 
SGK RỐI LOẠN TOAN KIỀM ĐHYHN RẤT HAY VÀ ĐẶC SẮC.pdf
SGK RỐI LOẠN TOAN KIỀM ĐHYHN RẤT HAY VÀ ĐẶC SẮC.pdfSGK RỐI LOẠN TOAN KIỀM ĐHYHN RẤT HAY VÀ ĐẶC SẮC.pdf
SGK RỐI LOẠN TOAN KIỀM ĐHYHN RẤT HAY VÀ ĐẶC SẮC.pdfHongBiThi1
 
Using Data Visualization in Public Health Communications
Using Data Visualization in Public Health CommunicationsUsing Data Visualization in Public Health Communications
Using Data Visualization in Public Health Communicationskatiequigley33
 
High-Performance Thin-Layer Chromatography (HPTLC)
High-Performance Thin-Layer Chromatography (HPTLC)High-Performance Thin-Layer Chromatography (HPTLC)
High-Performance Thin-Layer Chromatography (HPTLC)kishan singh tomar
 
DNA nucleotides Blast in NCBI and Phylogeny using MEGA Xi.pptx
DNA nucleotides Blast in NCBI and Phylogeny using MEGA Xi.pptxDNA nucleotides Blast in NCBI and Phylogeny using MEGA Xi.pptx
DNA nucleotides Blast in NCBI and Phylogeny using MEGA Xi.pptxMAsifAhmad
 
ANATOMICAL FAETURES OF BONES FOR NURSING STUDENTS .pptx
ANATOMICAL FAETURES OF BONES  FOR NURSING STUDENTS .pptxANATOMICAL FAETURES OF BONES  FOR NURSING STUDENTS .pptx
ANATOMICAL FAETURES OF BONES FOR NURSING STUDENTS .pptxWINCY THIRUMURUGAN
 
CONNECTIVE TISSUE (ANATOMY AND PHYSIOLOGY).pdf
CONNECTIVE TISSUE (ANATOMY AND PHYSIOLOGY).pdfCONNECTIVE TISSUE (ANATOMY AND PHYSIOLOGY).pdf
CONNECTIVE TISSUE (ANATOMY AND PHYSIOLOGY).pdfDolisha Warbi
 
Role of Soap based and synthetic or syndets bar
Role of  Soap based and synthetic or syndets barRole of  Soap based and synthetic or syndets bar
Role of Soap based and synthetic or syndets barmohitRahangdale
 
Unit I herbs as raw materials, biodynamic agriculture.ppt
Unit I herbs as raw materials, biodynamic agriculture.pptUnit I herbs as raw materials, biodynamic agriculture.ppt
Unit I herbs as raw materials, biodynamic agriculture.pptPradnya Wadekar
 

Dernier (20)

How to cure cirrhosis and chronic hepatitis naturally
How to cure cirrhosis and chronic hepatitis naturallyHow to cure cirrhosis and chronic hepatitis naturally
How to cure cirrhosis and chronic hepatitis naturally
 
FDMA FLAP - The first dorsal metacarpal artery (FDMA) flap is used mainly for...
FDMA FLAP - The first dorsal metacarpal artery (FDMA) flap is used mainly for...FDMA FLAP - The first dorsal metacarpal artery (FDMA) flap is used mainly for...
FDMA FLAP - The first dorsal metacarpal artery (FDMA) flap is used mainly for...
 
EXERCISE PERFORMANCE.pptx, Lung function
EXERCISE PERFORMANCE.pptx, Lung functionEXERCISE PERFORMANCE.pptx, Lung function
EXERCISE PERFORMANCE.pptx, Lung function
 
Physiology of Smooth Muscles -Mechanics of contraction and relaxation
Physiology of Smooth Muscles -Mechanics of contraction and relaxationPhysiology of Smooth Muscles -Mechanics of contraction and relaxation
Physiology of Smooth Muscles -Mechanics of contraction and relaxation
 
Trustworthiness of AI based predictions Aachen 2024
Trustworthiness of AI based predictions Aachen 2024Trustworthiness of AI based predictions Aachen 2024
Trustworthiness of AI based predictions Aachen 2024
 
Red Blood Cells_anemia & polycythemia.pdf
Red Blood Cells_anemia & polycythemia.pdfRed Blood Cells_anemia & polycythemia.pdf
Red Blood Cells_anemia & polycythemia.pdf
 
SGK LEUKEMIA KINH DÒNG BẠCH CÂU HẠT HAY.pdf
SGK LEUKEMIA KINH DÒNG BẠCH CÂU HẠT HAY.pdfSGK LEUKEMIA KINH DÒNG BẠCH CÂU HẠT HAY.pdf
SGK LEUKEMIA KINH DÒNG BẠCH CÂU HẠT HAY.pdf
 
Bulimia nervosa ( Eating Disorders) Mental Health Nursing.
Bulimia nervosa ( Eating Disorders) Mental Health Nursing.Bulimia nervosa ( Eating Disorders) Mental Health Nursing.
Bulimia nervosa ( Eating Disorders) Mental Health Nursing.
 
ORAL HYPOGLYCAEMIC AGENTS - PART 2.pptx
ORAL HYPOGLYCAEMIC AGENTS  - PART 2.pptxORAL HYPOGLYCAEMIC AGENTS  - PART 2.pptx
ORAL HYPOGLYCAEMIC AGENTS - PART 2.pptx
 
SGK RỐI LOẠN TOAN KIỀM ĐHYHN RẤT HAY VÀ ĐẶC SẮC.pdf
SGK RỐI LOẠN TOAN KIỀM ĐHYHN RẤT HAY VÀ ĐẶC SẮC.pdfSGK RỐI LOẠN TOAN KIỀM ĐHYHN RẤT HAY VÀ ĐẶC SẮC.pdf
SGK RỐI LOẠN TOAN KIỀM ĐHYHN RẤT HAY VÀ ĐẶC SẮC.pdf
 
Using Data Visualization in Public Health Communications
Using Data Visualization in Public Health CommunicationsUsing Data Visualization in Public Health Communications
Using Data Visualization in Public Health Communications
 
High-Performance Thin-Layer Chromatography (HPTLC)
High-Performance Thin-Layer Chromatography (HPTLC)High-Performance Thin-Layer Chromatography (HPTLC)
High-Performance Thin-Layer Chromatography (HPTLC)
 
GOUT UPDATE AHMED YEHIA 2024, case based approach with application of the lat...
GOUT UPDATE AHMED YEHIA 2024, case based approach with application of the lat...GOUT UPDATE AHMED YEHIA 2024, case based approach with application of the lat...
GOUT UPDATE AHMED YEHIA 2024, case based approach with application of the lat...
 
American College of physicians ACP high value care recommendations in rheumat...
American College of physicians ACP high value care recommendations in rheumat...American College of physicians ACP high value care recommendations in rheumat...
American College of physicians ACP high value care recommendations in rheumat...
 
DNA nucleotides Blast in NCBI and Phylogeny using MEGA Xi.pptx
DNA nucleotides Blast in NCBI and Phylogeny using MEGA Xi.pptxDNA nucleotides Blast in NCBI and Phylogeny using MEGA Xi.pptx
DNA nucleotides Blast in NCBI and Phylogeny using MEGA Xi.pptx
 
ANATOMICAL FAETURES OF BONES FOR NURSING STUDENTS .pptx
ANATOMICAL FAETURES OF BONES  FOR NURSING STUDENTS .pptxANATOMICAL FAETURES OF BONES  FOR NURSING STUDENTS .pptx
ANATOMICAL FAETURES OF BONES FOR NURSING STUDENTS .pptx
 
How to master Steroid (glucocorticoids) prescription, different scenarios, ca...
How to master Steroid (glucocorticoids) prescription, different scenarios, ca...How to master Steroid (glucocorticoids) prescription, different scenarios, ca...
How to master Steroid (glucocorticoids) prescription, different scenarios, ca...
 
CONNECTIVE TISSUE (ANATOMY AND PHYSIOLOGY).pdf
CONNECTIVE TISSUE (ANATOMY AND PHYSIOLOGY).pdfCONNECTIVE TISSUE (ANATOMY AND PHYSIOLOGY).pdf
CONNECTIVE TISSUE (ANATOMY AND PHYSIOLOGY).pdf
 
Role of Soap based and synthetic or syndets bar
Role of  Soap based and synthetic or syndets barRole of  Soap based and synthetic or syndets bar
Role of Soap based and synthetic or syndets bar
 
Unit I herbs as raw materials, biodynamic agriculture.ppt
Unit I herbs as raw materials, biodynamic agriculture.pptUnit I herbs as raw materials, biodynamic agriculture.ppt
Unit I herbs as raw materials, biodynamic agriculture.ppt
 

FreeSurfer Reader-3766

  • 1. Slicer Tutorial 6 Module: vtkFreeSurferReaders Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.
  • 2.
  • 3.
  • 4.
  • 5. Goal of this tutorial Guide you step-by-step through the process of loading and viewing FreeSurfer segmentation, surface reconstruction and parcellation results within Slicer.
  • 6.
  • 7.
  • 9.
  • 10.
  • 11. vtkFreeSurferReaders Module Select the Menu Modules in the Main Panel Select the category IO and the module vtkFreeSurferReaders
  • 12. vtkFreeSurferReaders Module The vtkFreeSurferReaders module appears in the Main Panel of Slicer. The Volumes tab comes up by default.
  • 13. Loading a Brain file Brain.mgz Skull Stripping and Noise Filtering Watershed algorithm Intensity corrected T1 volume FreeSurfer Pipeline
  • 14. Loading a Brain file Select the Tab Volumes in the FreeSurfer Module Click on Browse and select the subject bert Click on the mri folder to access the brain volume.
  • 15. Loading a Brain file Select the file brain.mgz Select the data type GrayScale Click Apply
  • 16. Loading a Brain file The volume Brain.mgz appears in the Viewer .
  • 17. Loading a Brain file Click on the V buttons in the Axial, Sagittal and Coronal views.
  • 18. Loading a Brain file The three anatomical slices appear in the 3D Viewer .
  • 19. Loading an ASEG file Aseg.mgz Segmentation Subcortical processing Intensity corrected T1 volume FreeSurfer Pipeline
  • 20. Loading an ASEG file Select the Tab Volumes in the FreeSurfer Module. Click on Browse and select the subject bert Click on the mri folder to access the aseg volume.
  • 21. Loading an ASEG file Select the file aseg.mgz Select the data type Label Map Click on Apply
  • 22. Loading an ASEG file The labels are superimposed on the gray level brain images. The volume aseg.mgz appears in the Viewer .
  • 23. Determining label numbers in an ASEG file # ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range 1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 2 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000 146.0000 3 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.0000 4 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.0000 5 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.0000 6 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 7 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.0000 8 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.0000 9 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.0000 10 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.0000 11 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.0000 12 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.0000 13 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.0000 14 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.0000 15 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.0000 16 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.0000 17 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.0000 18 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.0000 19 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.0000 20 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.0000 21 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.0000 22 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.0000 23 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.0000 24 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.0000 25 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.0000 26 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.0000 27 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.0000 28 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.0000 29 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.0000 30 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000 The file aseg.stats gives the list of the available segmented structures in the dataset. Example of the first 30 structures .
  • 24. Determining label numbers in an ASEG file # ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range 1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 2 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000 146.0000 3 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.0000 4 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.0000 5 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.0000 6 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 7 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.0000 8 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.0000 9 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.0000 10 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.0000 11 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.0000 12 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.0000 13 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.0000 14 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.0000 15 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.0000 16 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.0000 17 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.0000 18 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.0000 19 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.0000 20 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.0000 21 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.0000 22 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.0000 23 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.0000 24 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.0000 25 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.0000 26 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.0000 27 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.0000 28 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.0000 29 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.0000 30 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000 The label #10 represents the Left-Thalamus Proper. The corresponding segmented volume is available in the current dataset.
  • 25. Determining label numbers in an ASEG file # ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range 1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 2 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000 146.0000 3 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.0000 4 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.0000 5 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.0000 6 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.0000 7 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.0000 8 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.0000 9 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.0000 10 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.0000 11 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.0000 12 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.0000 13 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.0000 14 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.0000 15 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.0000 16 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.0000 17 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.0000 18 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.0000 19 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.0000 20 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.0000 21 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.0000 22 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.0000 23 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.0000 24 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.0000 25 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.0000 26 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.0000 27 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.0000 28 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.0000 29 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.0000 30 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000 The label #19 representing the Left-Insula. The corresponding segmented volume is not available in the current dataset.
  • 26.
  • 27. Overlay Brain and Segmentation Click on the button Bg (Background) and select the volume aseg in the Axial view.
  • 28. Overlay Brain and Segmentation Move the mouse over the labels in the Axial view.
  • 29. Overlay Brain and Segmentation The names of the labels appear in the window.
  • 30. Overlay Brain and Segmentation Find the labels corresponding to the Left Thalamus Proper , Left Caudate and Left Putamen in the three anatomical views.
  • 31. Overlay Brain and Segmentation Left Thalamus Proper = 10
  • 32. Overlay Brain and Segmentation Left Putamen = 12
  • 33. Overlay Brain and Segmentation Left Caudate = 11
  • 34. Overlay Brain and Segmentation Select View  3D in the MainMenu
  • 35. Overlay Brain and Segmentation Drag right mouse button down in the 3D Viewer to zoom in .
  • 36. Overlay Brain and Segmentation The Viewer displays a zoom view of the brain and aseg slices superimposed. Drag right mouse button up in the Viewer to zoom out .
  • 37.
  • 38. Building a single Model Select the module ModelMaker in the MainMenu Select the panel Create Select the Volume aseg and click on the button Label
  • 39. Building a single Model Slicer displays the Color Map corresponding to the structures that FreeSurfer can segment.
  • 40. Building a single Model Move the mouse over the table and select the label of the right hippocampus (label 53).
  • 41. Building a single Model The label of the right hippocampus appears in the Create panel. Click on Create to build the 3D model.
  • 42. Building a single Model The 3D model of the right hippocampus appears in the Viewer. Switch to the view 3D , and drag right mouse button down in the Viewer to zoom in.
  • 43. Building a single Model Slicer displays a zoom view of the right hippocampus .
  • 44. Building 3D Models Select the module ModelMaker in the MainMenu Select the panel Create Multiple
  • 45. Building 3D Models Select the Volume aseg and click on the button Starting Label The Panel Create Multiple provides the interface to build a set of continuous models from the values in the interval [Starting Label, Ending Label]
  • 46. Building 3D Models Click on the label corresponding to the Left Thalamus Proper (Label 10).
  • 47. Building 3D Models Click on the button Ending Label The value and the color of the selected label appear in the panel.
  • 48. Building 3D Models Click on the label corresponding to the Left Pallidum (Label 13).
  • 49. Building 3D Models Click on Create all to build the 3D models of the selected labels. Slicer reconstructs the 3D models from the labels 10,11,12 and 13.
  • 50. Building 3D Models The 3D models of the selected structures appear inside the Viewer.
  • 51. Building 3D Models Left click and move the mouse to orient the models in the Viewer
  • 52. Building 3D Models Click in the module Models in the Main Menu and select the panel Display. The list of models appears in the panel. Deselect the models of the Left Putamen and Left Caudate.
  • 53. Building 3D Models Slicer displays the left Thalamus Proper , left Pallidum and right Hippocampus in the Viewer.
  • 54. Building 3D Models Click on Show None to make all the models disappear from the Scene.
  • 55.
  • 56. Loading Surfaces Select the panel Models in the vtkFreeSurferReaders module. Click on Browse and select the surface lh.white in the directory subjects/bert/surf
  • 57. Loading Surfaces Click Apply to load the surface in Slicer. The name of the surface selected appears in the Models panel.
  • 58. Loading Surface The surface of the white matter of the left hemisphere appears in the Viewer.
  • 59. Parcellation Visualization In the panel Models click on aparc to select the parcellation map of the model lh.white Click on Apply to load the overlay.
  • 60. Parcellation Visualization Slicer displays the parcellation results overlaid on the white matter surface in the Viewer. Switch to 3D view in the main menu and zoom in the model.
  • 61. Parcellation Visualization Cortical parcellation of the white matter surface in the left hemisphere.
  • 62.
  • 63.
  • 64. Group Statistics Statistical Parametric Map Average Subject creation General Linear Modeling
  • 65. Group Statistics - example Statistical Parametric Map sigt_Age_dossthickness-100lh.w Average Subject creation lh.pial_avg For my cohort of x sujects, does cortical thickness vary with age? General Linear Modeling y_doss_thickness-100lh.fsgd
  • 66. Group Statistics Select the Tab Models in the vtkFreeSurferReaders module. Click on Browse and select the surface lh.pial_avg in the directory subjects/average/surf
  • 67. Group Statistics Select the Tab Display in the vtkFreeSurferReaders module. Click on Browse and select the overlay subjects/stats/sigt_Age_doss-thickness-100lh.w Click on Load Scalar File.
  • 68. Group Statistics Slicer displays the statistical map as an overlay superimposed on the average surface. Move the model with the mouse to update the Viewer display.
  • 69. Group Statistics Select the Panel Plot in the vtkFreeSurferReaders module. Click on Browse and select the file y_doss-thickness-100lh.fsgd in the directory subjects/stats.
  • 70. Group Statistics Select the Active Model lh.pial_avg in the list of models. Click on Apply to load the Group Statistics results.
  • 71. Group Statistics Slicer displays statistical distribution of the cortical thickness of the left hemisphere parameterized by the age of the population.
  • 72. Group Statistics Select the Mode subject in the Group Statistics Window.
  • 73. Group Statistics Slicer displays the subjects included in the Statistical Analysis. Move the mouse over the subjects table and select the subject #108.
  • 74. Group Statistics A red circle shows the position of the subject #108 in the analysis.
  • 75. Group Statistics The Configure Classes menu displays the visualization options of the population.
  • 76. Group Statistics Select the pattern diamond and the color black for the male subjects. Select the pattern circle and the color purple for the female subjects.
  • 77. Group Statistics Slicer updates the interface with the new configuration parameters.
  • 78. Group Statistics To generate a plot for a particular vertex, select a point by clicking on the parametric map at that vertex on the 3D model in the Viewer
  • 79. Group Statistics Slicer updates the thickness results with the values corresponding to the selected vertex.
  • 80.