1. 3D Visualization of FreeSurfer Data
Sonia Pujol, Ph.D.
Silas Mann, B.Sc.
Randy Gollub, MD., Ph.D.
Surgical Planning Laboratory
Athinoula A. Martinos Center
Harvard University

2. Acknowledgements National Alliance for Medical Image Computing
NIH U54EB005149
Neuroimage Analysis Center
NIH P41RR013218
Morphometry Biomedical Informatics Research Network
NIH U24RRO21382
Surgical Planning Laboratory (BWH)
Thanks to Nicole Aucoin
Center for Functional Neuroimaging Technology
NIH P41RR14075

3. Learning Objective
Guide you step-by-step through the process of loading and viewing FreeSurfer segmentations, surface reconstructions, and parcellation results within Slicer3.

4. Prerequisites
This tutorial assumes that you have completed the course Data Loading and Visualization.
Tutorials for Slicer3 are available on the Slicer101 page:

5. Prerequisites
This tutorial assumes a working knowledge of how to use FreeSurfer to generate segmentation and surface files.
Tutorials for FreeSurfer are available at the following location:

6. Materials
This tutorial requires the installation of the Slicer3 software and the tutorial dataset. These materials are available at the following locations:
• Slicer3 download page (Slicer 3.2)
Note that the training tutorial website has not been updated yet with this particular dataset.
Disclaimer: It is the responsibility of the user of Slicer to comply with both the terms of the license and with the applicable laws, regulations, and rules.

7. Materials
This tutorial makes use of the same T1 weighted image dataset (bert) that is used for the FreeSurfer tutorial available at the following location:
If you already have the FreeSurfer subject ‘bert’ on your computer, then just download the file ‘slicerGenericScene.mrml’
If you don’t have the FreeSurfer tutorial dataset known as ‘bert’ on your computer, then download the archive below:
Note that the training tutorial website has not been updated yet with this particular dataset.

8. Overview From FreeSurfer, Slicer3 can load:
Brain volumes
ASEG volumes
Surfaces
Parcellation Maps
All of the above, via a scene file

9. Overview Part 1: Loading and Visualizing FreeSurfer Volumes
Part 2: Building 3D Models
Part 3: Loading FreeSurfer Surfaces
and Visualizing Parcellation Maps
Part 4:Automatic Data Loading via a Generic Scene File

10. Part 1: Loading and Visualizing FreeSurfer Volumes

11. Skull Stripping and Noise Filtering
Loading a Brain File
FreeSurfer pipeline
Intensity corrected
T1 volume
Skull Stripping and Noise Filtering
Watershed Algorithm
brain.mgz

12. Loading a Brain File
Select Volumes from the Module menu

13. Loading a Brain File
Click on Select Volume File

14. Loading a Brain File
Browse to find the dataset brain.mgz located in the directory
/subjects/bert/mri/
and click on Open

15. Loading a Brain File
Choose Image Origin: Centered and click Apply

16. Loading a Brain File
The volume brain.mgz appears in the Slice Viewer

17. Loading a Brain File
Click on the links icon to link the three anatomical slices.
Click on the Slice Visibility icon to display the slices in the 3D Viewer

18. Loading a Brain File
The three anatomical slices appear in the 3D Viewer

19. Subcortical processing
Loading an ASEG File
FreeSurfer pipeline
Intensity corrected
T1 volume
Subcortical processing
Segmentation
aseg.mgz

20. Loading an ASEG File
Click on Select Volume File, and browse to find the dataset aseg.mgz located in the directory
/subjects/bert/mri/
and click on Open

21. Select Label Map and click on Apply
Loading an ASEG File
Select Label Map and click on Apply

22. Loading an ASEG File The volume aseg.mgz appears in the Viewer
The labels are superimposed on the gray brain images

23. Mouse over the labels in the Axial view
Overlay Brain & Segmentation
Mouse over the labels in the Axial view

24. The names of the labels appear in the window
Overlay Brain & Segmentation
Overlay Brain & Segmentation
The names of the labels appear in the window

25. Overlay Brain & Segmentation
Find the labels corresponding to the Left Thalamus Proper, the Left Caudate, and the Left Putamen in the three anatomical views

26. Overlay Brain & Segmentation
Left Thalamus Proper = #10
Left Putamen = #12
Left Caudate = #11

27. Part 2: Building
3D Models

28. Building 3D Models • Building Multiple Models
• Building a Single Model
• Building Multiple Models

29. Select the module Model Maker from the category Model Generation
Building a Single Model
Select the module Model Maker from the category Model Generation

30. Building a Single Model
Choose Input Volume: aseg.mgz
Select Models: Create New ModelHierarchy

31. Building a Single Model
Type in label #53, which corresponds to the label for the Right Hippocampus
Click on Apply

32. Building a Single Model
The 3-dimensional model of the Right Hippocampus appears in the 3D Viewer

33. Building 3D Models • Building Multiple Models
• Building a Single Model
• Building Multiple Models

34. Building Multiple Models
Delete label #53, and set the Start Label to label #10, which corresponds to the Left Thalamus Proper
Set the End Label to label #13, which corresponds to the Left Pallidum
Check Joint Smoothing and click on Apply

35. Building Multiple Models
The 3-dimensional models of the Left Thalamus Proper (label #10), Left Caudate (label #11), Left Putamen (label #12), and Left Pallidum (label #13) appear in the 3D Viewer

36. Part 3: Loading FreeSurfer Surfaces and Visualizing Parcellation Maps

37. Select the module Models from the Module menu
Building Multiple Models
Select the module Models from the Module menu

38. Loading Surfaces
Click on Load Model, and browse to find the surface lh.white located in the directory
/subjects/bert/surf/
Click on Open

39. Loading Surfaces
The surface of the White Matter of the Left Hemisphere appears in the 3D Viewer

40. Visualizing Parcellation Maps
Expand the tab Hierarchy & Display
and select the surface
lh.white under the tab ModelDisplay

41. Visualizing Parcellation Maps
Click on Load FreeSurfer Overlay, browse to find the Parcellation Map lh.aparc.annot located in the directory
/subjects/bert/label/
and click on Open

42. Visualizing Parcellation Maps
The Parcellation Map is overlaid on the White Matter surface in the 3D Viewer

43. Part 4: Automatic Data Loading via a Generic Scene File

44. Loading a Generic Scene File
Click on Close Scene in the File menu to close the current scene
Click OK to confirm

45. Loading a Generic Scene File
• The generic scene file works by looking in the subject directory created by FreeSurfer, and loading all available volumes and models based on known subdirectory names and filenames.
• The file slicerGenericScene.mrml will work properly if the subdirectory names and filenames have not been changed by the user.

46. Loading a Generic Scene File
Copy the file slicerGenericScene.mrml into the directory /subjects/ of our tutorial dataset.
/subjects/

47. Loading a Generic Scene File
Copy the file slicerGenericScene.mrml located in the directory /subjects/, into the directory /subjects/bert/ of our sample subject.
/subjects/bert/

48. Loading a Generic Scene File
Rename the file ‘slicerGenericScene.mrml’ located in the directory /subjects/bert/ ‘slicerBertScene.mrml’
/subjects/bert/

49. Loading a Generic Scene File
Click on Load Scene in the File menu, and select the scene
slicerBertScene.mrml located in the directory /subjects/bert/

50. Loading a Generic Scene File
The scene appears with a list of files which have been automatically loaded from the subject directory bert.

51. Loading a Generic Scene File
Select the mode 3D only layout from the Viewer menu

52. Loading a Generic Scene File
Select the module Models, and expand the tab Hierarchy & Display to display the list of models that were loaded

53. Loading a Generic Scene File
Select the surface lh_pial, and turn on the visibility of the model

54. Loading a Generic Scene File
Slicer displays the left hemisphere pial surface in the 3D viewer

55. Loading a Generic Scene File
The generic scene includes three snapshots that provide a variety of scene setups:
Left and Right Annotations
Left and Right Pial curve
Left and right white sulc

56. Loading a Generic Scene File
Click on the restore snapshots icon, select the snapshot Left and right white sulc, and click on restore

57. Loading a Generic Scene File
The snapshot displays the left and right sulci using the GreenRed colorscheme.

58. Summary From FreeSurfer, Slicer3 can load:
Brain volumes
ASEG volumes
Surfaces
Parcellation Maps
All of the above, via a scene file

59. Conclusion
• 3D visualization of brain segmented surfaces and parcellation maps
• Intuitive graphical user interface to interact with FreeSurfer data
• Multi platforms open-source environment