Slicer Tutorial 6 Module vtk Free Surfer Readers

Slicer Tutorial 6 Module: vtk. Free. Surfer. Readers Sonia Pujol, Ph. D. Randy Gollub, M. D. , Ph. D. Surgical Planning Laboratory -1 - http: //www. slicer. org Brigham and Women’s Hospital

Acknowledgments National Alliance for Medical Image Computing NIH U 54 EB 005149 Neuroimage Analysis Center NIH P 41 RR 013218 Center for Functional Neuroimaging Technologies NIH P 41 RR 14075 Morphometry Biomedical Informatics Research Network NIH U 24 RRO 21382 Surgical Planning Laboratory Thanks to Nicole Aucoin Surgical Planning Laboratory -2 - http: //www. slicer. org Brigham and Women’s Hospital

Disclaimer It is the responsibility of the user of 3 DSlicer and Free. Surfer to comply with both the terms of the licenses and with the applicable laws, regulations and rules. Surgical Planning Laboratory -3 - http: //www. slicer. org Brigham and Women’s Hospital

Materials Needed • Slicer 2. 5 MGH http: //www. na-mic. org/Wiki/index. php/Slicer: Slicer 2. 5 MGH_Getting_Started • Free Surfer Sample Data: Freesurfer. Subjects. zip http: //www. na-mic. org/Wiki/index. php/Slicer: Workshops: User_Training_101 Surgical Planning Laboratory -4 - http: //www. slicer. org Brigham and Women’s Hospital

Goal of this tutorial Guide you step-by-step through the process of loading and viewing Free. Surfer segmentation, surface reconstruction and parcellation results within Slicer. Surgical Planning Laboratory -5 - http: //www. slicer. org Brigham and Women’s Hospital

Prerequisites This tutorial assumes a working knowledge of how to use Free. Surfer to generate the segmentation and surface files. Tutorial materials for Free. Surfer are available at https: //surfer. nmr. mgh. harvard. edu/fswiki https: //surfer. nmr. mgh. harvard. edu/docs/f tp/pub/docs/fs. Tutorial/ Surgical Planning Laboratory -6 - http: //www. slicer. org Brigham and Women’s Hospital

Prerequisites This tutorial assumes a basic knowledge of how to use 3 DSlicer Training 1: Loading and Viewing Data Slicer Training 7: Saving Data http: //www. namic. org/Wiki/index. php/ Slicer: Workshops: User_Training_101 Surgical Planning Laboratory -7 - http: //www. slicer. org Brigham and Women’s Hospital

vtk. Free. Surfer. Readers Module Surgical Planning Laboratory -8 - http: //www. slicer. org Brigham and Women’s Hospital

Loading Free. Surfer Data Slicer can load • Brain Volumes …………. • ASEG Volumes …………… • Surfaces………………… • Overlays …………………. Surgical Planning Laboratory -9 - http: //www. slicer. org Brigham and Women’s Hospital

Overview of Training 6 • Part 1: Loading Free. Surfer Volumes • Part 2: Overlay Brain and Segmentation • Part 3: Building 3 D Models • Part 4: Loading Surfaces • Part 5: Group Statistics Surgical Planning Laboratory -10 - http: //www. slicer. org Brigham and Women’s Hospital

vtk. Free. Surfer. Readers Module Select the Menu Modules in the Main Panel Select the category IO and the module vtk. Free. Surfer. Readers Surgical Planning Laboratory -11 - http: //www. slicer. org Brigham and Women’s Hospital

vtk. Free. Surfer. Readers Module The vtk. Free. Surfer. Readers module appears in the Main Panel of Slicer. The Volumes tab comes up by default. Surgical Planning Laboratory -12 - http: //www. slicer. org Brigham and Women’s Hospital

Loading a Brain file Free. Surfer Pipeline Intensity corrected T 1 volume Skull Stripping and Noise Filtering Watershed algorithm Brain. mgz Surgical Planning Laboratory -13 - http: //www. slicer. org Brigham and Women’s Hospital

Loading a Brain file Select the Tab Volumes in the Free. Surfer Module Click on Browse and select the subject bert Click on the mri folder to access the brain volume. Surgical Planning Laboratory -14 - http: //www. slicer. org Brigham and Women’s Hospital

Loading a Brain file Select the file brain. mgz Select the data type Gray. Scale Click Apply Surgical Planning Laboratory -15 - http: //www. slicer. org Brigham and Women’s Hospital

Loading a Brain file The volume Brain. mgz appears in the Viewer. Surgical Planning Laboratory -16 - http: //www. slicer. org Brigham and Women’s Hospital

Loading a Brain file Click on the V buttons in the Axial, Sagittal and Coronal views. Surgical Planning Laboratory -17 - http: //www. slicer. org Brigham and Women’s Hospital

Loading a Brain file The three anatomical slices appear in the 3 D Viewer. Surgical Planning Laboratory -18 - http: //www. slicer. org Brigham and Women’s Hospital

Loading an ASEG file Free. Surfer Pipeline Intensity corrected T 1 volume Subcortical processing Segmentation Aseg. mgz Surgical Planning Laboratory -19 - http: //www. slicer. org Brigham and Women’s Hospital

Loading an ASEG file Select the Tab Volumes in the Free. Surfer Module. Click on Browse and select the subject bert Click on the mri folder to access the aseg volume. Surgical Planning Laboratory -20 - http: //www. slicer. org Brigham and Women’s Hospital

Loading an ASEG file Select the file aseg. mgz Select the data type Label Map Click on Apply Surgical Planning Laboratory -21 - http: //www. slicer. org Brigham and Women’s Hospital

Loading an ASEG file The volume aseg. mgz appears in the Viewer. The labels are superimposed on the gray level brain images. Surgical Planning Laboratory -22 - http: //www. slicer. org Brigham and Women’s Hospital

Determining label numbers in an ASEG file # Col. Headers Index Seg. Id NVoxels Volume_mm 3 Seg. Name Mean Std. Dev Min Max Range 1 1 0 0. 0 Left-Cerebral-Exterior 0. 0000 2 2 245171. 0 Left-Cerebral-White-Matter 121. 7886 8. 0072 40. 0000 186. 0000 146. 0000 3 3 287069. 0 Left-Cerebral-Cortex 91. 3494 13. 8505 31. 0000 220. 0000 189. 0000 4 4 6876. 0 Left-Lateral-Ventricle 48. 2126 14. 3628 25. 0000 106. 0000 81. 0000 5 5 200. 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 7 7 10514. 0 Left-Cerebellum-White-Matter 120. 4405 8. 5863 43. 0000 134. 0000 91. 0000 8 8 66561. 0 Left-Cerebellum-Cortex 98. 8117 14. 1726 32. 0000 211. 0000 179. 0000 9 9 0 0. 0 Left-Thalamus 0. 0000 10 10 9887. 0 Left-Thalamus-Proper 113. 5839 10. 3047 45. 0000 133. 0000 88. 0000 11 11 3819. 0 Left-Caudate 102. 9627 12. 1416 62. 0000 132. 0000 70. 0000 12 12 6755. 0 Left-Putamen 110. 0479 7. 4787 76. 0000 132. 0000 56. 0000 13 13 2229. 0 Left-Pallidum 122. 5797 4. 2841 105. 0000 134. 0000 29. 0000 14 14 793. 0 3 rd-Ventricle 54. 2582 15. 3296 28. 0000 93. 0000 65. 0000 15 15 1819. 0 4 th-Ventricle 51. 8305 15. 5400 27. 0000 108. 0000 81. 0000 16 16 26616. 0 Brain-Stem 113. 1949 12. 7048 39. 0000 136. 0000 97. 0000 17 17 4489. 0 Left-Hippocampus 96. 0929 8. 6315 56. 0000 122. 0000 66. 0000 18 18 1869. 0 Left-Amygdala 94. 8671 8. 2028 61. 0000 118. 0000 57. 0000 19 19 0 0. 0 Left-Insula 0. 0000 20 20 0 0. 0 Left-Operculum 0. 0000 21 21 0 0. 0 Line-1 0. 0000 22 22 0 0. 0 Line-2 0. 0000 23 23 0 0. 0 Line-3 0. 0000 24 24 1611. 0 CSF 59. 9684 15. 4368 30. 0000 107. 0000 77. 0000 25 25 0 0. 0 Left-Lesion 0. 0000 26 26 733. 0 Left-Accumbens-area 97. 8124 6. 7471 67. 0000 121. 0000 54. 0000 27 27 0 0. 0 Left-Substancia-Nigra 0. 0000 28 28 3957. 0 Left-Ventral. DC 117. 4001 10. 5813 47. 0000 135. 0000 88. 0000 29 29 0 0. 0 Left-undetermined 0. 0000 30 30 56 56. 0 Left-vessel 81. 5250 7. 9485 62. 0000 97. 0000 35. 0000 Surgical Planning Laboratory -23 - http: //www. slicer. org The file aseg. stats gives the list of the available segmented structures in the dataset. Example of the first 30 structures. Brigham and Women’s Hospital

Determining label numbers in an ASEG file # Col. Headers Index Seg. Id NVoxels Volume_mm 3 Seg. Name Mean Std. Dev Min Max Range 1 1 0 0. 0 Left-Cerebral-Exterior 0. 0000 2 2 245171. 0 Left-Cerebral-White-Matter 121. 7886 8. 0072 40. 0000 186. 0000 146. 0000 3 3 287069. 0 Left-Cerebral-Cortex 91. 3494 13. 8505 31. 0000 220. 0000 189. 0000 4 4 6876. 0 Left-Lateral-Ventricle 48. 2126 14. 3628 25. 0000 106. 0000 81. 0000 5 5 200. 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 7 7 10514. 0 Left-Cerebellum-White-Matter 120. 4405 8. 5863 43. 0000 134. 0000 91. 0000 8 8 66561. 0 Left-Cerebellum-Cortex 98. 8117 14. 1726 32. 0000 211. 0000 179. 0000 9 9 0 0. 0 Left-Thalamus 0. 0000 10 10 9887. 0 Left-Thalamus-Proper 113. 5839 10. 3047 45. 0000 133. 0000 88. 0000 11 11 3819. 0 Left-Caudate 102. 9627 12. 1416 62. 0000 132. 0000 70. 0000 12 12 6755. 0 Left-Putamen 110. 0479 7. 4787 76. 0000 132. 0000 56. 0000 13 13 2229. 0 Left-Pallidum 122. 5797 4. 2841 105. 0000 134. 0000 29. 0000 14 14 793. 0 3 rd-Ventricle 54. 2582 15. 3296 28. 0000 93. 0000 65. 0000 15 15 1819. 0 4 th-Ventricle 51. 8305 15. 5400 27. 0000 108. 0000 81. 0000 16 16 26616. 0 Brain-Stem 113. 1949 12. 7048 39. 0000 136. 0000 97. 0000 17 17 4489. 0 Left-Hippocampus 96. 0929 8. 6315 56. 0000 122. 0000 66. 0000 18 18 1869. 0 Left-Amygdala 94. 8671 8. 2028 61. 0000 118. 0000 57. 0000 19 19 0 0. 0 Left-Insula 0. 0000 20 20 0 0. 0 Left-Operculum 0. 0000 21 21 0 0. 0 Line-1 0. 0000 22 22 0 0. 0 Line-2 0. 0000 23 23 0 0. 0 Line-3 0. 0000 24 24 1611. 0 CSF 59. 9684 15. 4368 30. 0000 107. 0000 77. 0000 25 25 0 0. 0 Left-Lesion 0. 0000 26 26 733. 0 Left-Accumbens-area 97. 8124 6. 7471 67. 0000 121. 0000 54. 0000 27 27 0 0. 0 Left-Substancia-Nigra 0. 0000 28 28 3957. 0 Left-Ventral. DC 117. 4001 10. 5813 47. 0000 135. 0000 88. 0000 29 29 0 0. 0 Left-undetermined 0. 0000 30 30 56 56. 0 Left-vessel 81. 5250 7. 9485 62. 0000 97. 0000 35. 0000 Surgical Planning Laboratory -24 - http: //www. slicer. org The label #10 represents the Left- Thalamus Proper. The corresponding segmented volume is available in the current dataset. Brigham and Women’s Hospital

Determining label numbers in an ASEG file # Col. Headers Index Seg. Id NVoxels Volume_mm 3 Seg. Name Mean Std. Dev Min Max Range 1 1 0 0. 0 Left-Cerebral-Exterior 0. 0000 2 2 245171. 0 Left-Cerebral-White-Matter 121. 7886 8. 0072 40. 0000 186. 0000 146. 0000 3 3 287069. 0 Left-Cerebral-Cortex 91. 3494 13. 8505 31. 0000 220. 0000 189. 0000 4 4 6876. 0 Left-Lateral-Ventricle 48. 2126 14. 3628 25. 0000 106. 0000 81. 0000 5 5 200. 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 7 7 10514. 0 Left-Cerebellum-White-Matter 120. 4405 8. 5863 43. 0000 134. 0000 91. 0000 8 8 66561. 0 Left-Cerebellum-Cortex 98. 8117 14. 1726 32. 0000 211. 0000 179. 0000 9 9 0 0. 0 Left-Thalamus 0. 0000 10 10 9887. 0 Left-Thalamus-Proper 113. 5839 10. 3047 45. 0000 133. 0000 88. 0000 11 11 3819. 0 Left-Caudate 102. 9627 12. 1416 62. 0000 132. 0000 70. 0000 12 12 6755. 0 Left-Putamen 110. 0479 7. 4787 76. 0000 132. 0000 56. 0000 13 13 2229. 0 Left-Pallidum 122. 5797 4. 2841 105. 0000 134. 0000 29. 0000 14 14 793. 0 3 rd-Ventricle 54. 2582 15. 3296 28. 0000 93. 0000 65. 0000 15 15 1819. 0 4 th-Ventricle 51. 8305 15. 5400 27. 0000 108. 0000 81. 0000 16 16 26616. 0 Brain-Stem 113. 1949 12. 7048 39. 0000 136. 0000 97. 0000 17 17 4489. 0 Left-Hippocampus 96. 0929 8. 6315 56. 0000 122. 0000 66. 0000 18 18 1869. 0 Left-Amygdala 94. 8671 8. 2028 61. 0000 118. 0000 57. 0000 19 19 0 0. 0 Left-Insula 0. 0000 20 20 0 0. 0 Left-Operculum 0. 0000 21 21 0 0. 0 Line-1 0. 0000 22 22 0 0. 0 Line-2 0. 0000 23 23 0 0. 0 Line-3 0. 0000 24 24 1611. 0 CSF 59. 9684 15. 4368 30. 0000 107. 0000 77. 0000 25 25 0 0. 0 Left-Lesion 0. 0000 26 26 733. 0 Left-Accumbens-area 97. 8124 6. 7471 67. 0000 121. 0000 54. 0000 27 27 0 0. 0 Left-Substancia-Nigra 0. 0000 28 28 3957. 0 Left-Ventral. DC 117. 4001 10. 5813 47. 0000 135. 0000 88. 0000 29 29 0 0. 0 Left-undetermined 0. 0000 30 30 56 56. 0 Left-vessel 81. 5250 7. 9485 62. 0000 97. 0000 35. 0000 Surgical Planning Laboratory -25 - http: //www. slicer. org The label #19 representing the Left-Insula. The corresponding segmented volume is not available in the current dataset. Brigham and Women’s Hospital

Overview of Training 6 • Part 1: Loading Free. Surfer Volumes • Part 2: Overlay Brain and Segmentation • Part 3: Building 3 D Models • Part 4: Loading Surfaces • Part 5: Group Statistics Surgical Planning Laboratory -26 - http: //www. slicer. org Brigham and Women’s Hospital

Overlay Brain and Segmentation Click on the button Bg (Background) and select the volume aseg in the Axial view. Surgical Planning Laboratory -27 - http: //www. slicer. org Brigham and Women’s Hospital

Overlay Brain and Segmentation Move the mouse over the labels in the Axial view. Surgical Planning Laboratory -28 - http: //www. slicer. org Brigham and Women’s Hospital

Overlay Brain and Segmentation The names of the labels appear in the window. Surgical Planning Laboratory -29 - http: //www. slicer. org Brigham and Women’s Hospital

Overlay Brain and Segmentation Find the labels corresponding to the Left Thalamus Proper, Left Caudate and Left Putamen in the three anatomical views. Surgical Planning Laboratory -30 - http: //www. slicer. org Brigham and Women’s Hospital

Overlay Brain and Segmentation Left Thalamus Proper = 10 Surgical Planning Laboratory -31 - http: //www. slicer. org Brigham and Women’s Hospital

Overlay Brain and Segmentation Left Putamen = 12 Surgical Planning Laboratory -32 - http: //www. slicer. org Brigham and Women’s Hospital

Overlay Brain and Segmentation Left Caudate = 11 Surgical Planning Laboratory -33 - http: //www. slicer. org Brigham and Women’s Hospital

Overlay Brain and Segmentation Select View 3 D in the Main. Menu Surgical Planning Laboratory -34 - http: //www. slicer. org Brigham and Women’s Hospital

Overlay Brain and Segmentation Drag right mouse button down in the 3 D Viewer to zoom in. Surgical Planning Laboratory -35 - http: //www. slicer. org Brigham and Women’s Hospital

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. Surgical Planning Laboratory -36 - http: //www. slicer. org Brigham and Women’s Hospital

Overview of Training 6 • Part 1: Loading Free. Surfer Volumes • Part 2: Overlay Brain and Segmentation • Part 3: Building 3 D Models • Part 4: Loading Surfaces • Part 5: Group Statistics Surgical Planning Laboratory -37 - http: //www. slicer. org Brigham and Women’s Hospital

Building a single Model Select the module Model. Maker in the Main. Menu Select the panel Create Select the Volume aseg and click on the button Label Surgical Planning Laboratory -38 - http: //www. slicer. org Brigham and Women’s Hospital

Building a single Model Slicer displays the Color Map corresponding to the structures that Free. Surfer can segment. Surgical Planning Laboratory -39 - http: //www. slicer. org Brigham and Women’s Hospital

Building a single Model Move the mouse over the table and select the label of the right hippocampus (label 53). Surgical Planning Laboratory -40 - http: //www. slicer. org Brigham and Women’s Hospital

Building a single Model The label of the right hippocampus appears in the Create panel. Click on Create to build the 3 D model. Surgical Planning Laboratory -41 - http: //www. slicer. org Brigham and Women’s Hospital

Building a single Model The 3 D model of the right hippocampus appears in the Viewer. Switch to the view 3 D, and drag right mouse button down in the Viewer to zoom in. Surgical Planning Laboratory -42 - http: //www. slicer. org Brigham and Women’s Hospital

Building a single Model Slicer displays a zoom view of the right hippocampus. Surgical Planning Laboratory -43 - http: //www. slicer. org Brigham and Women’s Hospital

Building 3 D Models Select the module Model. Maker in the Main. Menu Select the panel Create Multiple Surgical Planning Laboratory -44 - http: //www. slicer. org Brigham and Women’s Hospital

Building 3 D Models The Panel Create Multiple provides the interface to build a set of continuous models from the values in the interval [Starting Label, Ending Label] Select the Volume aseg and click on the button Starting Label Surgical Planning Laboratory -45 - http: //www. slicer. org Brigham and Women’s Hospital

Building 3 D Models Click on the label corresponding to the Left Thalamus Proper (Label 10). Surgical Planning Laboratory -46 - http: //www. slicer. org Brigham and Women’s Hospital

Building 3 D Models The value and the color of the selected label appear in the panel. Click on the button Ending Label Surgical Planning Laboratory -47 - http: //www. slicer. org Brigham and Women’s Hospital

Building 3 D Models Click on the label corresponding to the Left Pallidum (Label 13). Surgical Planning Laboratory -48 - http: //www. slicer. org Brigham and Women’s Hospital

Building 3 D Models Click on Create all to build the 3 D models of the selected labels. Slicer reconstructs the 3 D models from the labels 10, 11, 12 and 13. Surgical Planning Laboratory -49 - http: //www. slicer. org Brigham and Women’s Hospital

Building 3 D Models The 3 D models of the selected structures appear inside the Viewer. Surgical Planning Laboratory -50 - http: //www. slicer. org Brigham and Women’s Hospital

Building 3 D Models Left click and move the mouse to orient the models in the Viewer Surgical Planning Laboratory -51 - http: //www. slicer. org Brigham and Women’s Hospital

Building 3 D 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. Surgical Planning Laboratory -52 - http: //www. slicer. org Brigham and Women’s Hospital

Building 3 D Models Slicer displays the left Thalamus Proper, left Pallidum and right Hippocampus in the Viewer. Surgical Planning Laboratory -53 - http: //www. slicer. org Brigham and Women’s Hospital

Building 3 D Models Click on Show None to make all the models disappear from the Scene. Surgical Planning Laboratory -54 - http: //www. slicer. org Brigham and Women’s Hospital

Overview of Training 6 • Part 1: Loading Free. Surfer Volumes • Part 2: Overlay Brain and Segmentation • Part 3: Building 3 D Models • Part 4: Loading Surfaces • Part 5: Group Statistics Surgical Planning Laboratory -55 - http: //www. slicer. org Brigham and Women’s Hospital

Loading Surfaces Select the panel Models in the vtk. Free. Surfer. Readers module. Click on Browse and select the surface lh. white in the directory subjects/bert/surf Surgical Planning Laboratory -56 - http: //www. slicer. org Brigham and Women’s Hospital

Loading Surfaces The name of the surface selected appears in the Models panel. Click Apply to load the surface in Slicer. Surgical Planning Laboratory -57 - http: //www. slicer. org Brigham and Women’s Hospital

Loading Surface The surface of the white matter of the left hemisphere appears in the Viewer. Surgical Planning Laboratory -58 - http: //www. slicer. org Brigham and Women’s Hospital

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. Surgical Planning Laboratory -59 - http: //www. slicer. org Brigham and Women’s Hospital

Parcellation Visualization Slicer displays the parcellation results overlaid on the white matter surface in the Viewer. Switch to 3 D view in the main menu and zoom in the model. Surgical Planning Laboratory -60 - http: //www. slicer. org Brigham and Women’s Hospital

Parcellation Visualization Cortical parcellation of the white matter surface in the left hemisphere. Surgical Planning Laboratory -61 - http: //www. slicer. org Brigham and Women’s Hospital

Overview of Training 6 • Part 1: Loading Free. Surfer Volumes • Part 2: Overlay Brain and Segmentation • Part 3: Building 3 D Models • Part 4: Loading Surfaces • Part 5: Group Statistics Surgical Planning Laboratory -62 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics • After completion of surface reconstruction for all subjects in a study, Free. Surfer can perform group averaging and statistical inference of the cortical surface measurements such as thickness. • The observed data is a set of cortical surface measurements at each vertex for each subject in the group. • The process fits a General Linear Model at each vertex to summarize the data from all the subjects. • The group analysis results in a statistical parametric map that can be loaded into Slicer for visualisation as an overlay on the average surface. Surgical Planning Laboratory -63 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics Average Subject creation General Linear Modeling Statistical Parametric Map Surgical Planning Laboratory -64 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics - example For my cohort of x sujects, does cortical thickness vary with age? Average Subject creation lh. pial_avg General Linear Modeling y_doss_thickness-100 lh. fsgd Statistical Parametric Map sigt_Age_dossthickness-100 lh. w Surgical Planning Laboratory -65 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics Select the Tab Models in the vtk. Free. Surfer. Readers module. Click on Browse and select the surface lh. pial_avg in the directory subjects/average/surf Surgical Planning Laboratory -66 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics Select the Tab Display in the vtk. Free. Surfer. Readers module. Click on Browse and select the overlay subjects/stats/sigt_Age_dossthickness-100 lh. w Click on Load Scalar File. Surgical Planning Laboratory -67 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics Move the model with the mouse to update the Viewer display. Slicer displays the statistical map as an overlay superimposed on the average surface. Surgical Planning Laboratory -68 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics Select the Panel Plot in the vtk. Free. Surfer. Readers module. Click on Browse and select the file y_doss-thickness-100 lh. fsgd in the directory subjects/stats. Surgical Planning Laboratory -69 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics Select the Active Model lh. pial_avg in the list of models. Click on Apply to load the Group Statistics results. Surgical Planning Laboratory -70 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics Slicer displays statistical distribution of the cortical thickness of the left hemisphere parameterized by the age of the population. Surgical Planning Laboratory -71 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics Select the Mode subject in the Group Statistics Window. Surgical Planning Laboratory -72 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics Slicer displays the subjects included in the Statistical Analysis. Move the mouse over the subjects table and select the subject #108. Surgical Planning Laboratory -73 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics A red circle shows the position of the subject #108 in the analysis. Surgical Planning Laboratory -74 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics The Configure Classes menu displays the visualization options of the population. Surgical Planning Laboratory -75 - http: //www. slicer. org Brigham and Women’s Hospital

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. Surgical Planning Laboratory -76 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics Slicer updates the interface with the new configuration parameters. Surgical Planning Laboratory -77 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics To generate a plot for a particular vertex, select a point by clicking on the parametric map at that vertex on the 3 D model in the Viewer Surgical Planning Laboratory -78 - http: //www. slicer. org Brigham and Women’s Hospital

Group Statistics Slicer updates the thickness results with the values corresponding to the selected vertex. Surgical Planning Laboratory -79 - http: //www. slicer. org Brigham and Women’s Hospital

Conclusion • 3 D visualization of brain segmented surfaces, parcellation maps and statistical results from Free. Surfer • Intuitive graphical user interface to interact with the data • Open-Source environment Surgical Planning Laboratory -80 - http: //www. slicer. org Brigham and Women’s Hospital