3D Visualization of FreeSurfer Data
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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. Acknowledgements. National Alliance for Medical Image Computing NIH U54EB005149 Neuroimage Analysis Center

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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


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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


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Learning Objective

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


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Prerequisites

This tutorial assumes that you have completed the course Data Loading and Visualization.

Tutorials for Slicer3 are available on the Slicer101 page:

http://www.na-mic.org/Wiki/index.php/Slicer3.2:Training


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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:

http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials/


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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)

http://www.slicer.org/pages/Downloads

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.


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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:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial

If you already have the FreeSurfer subject ‘bert’ on your computer, then just download the file ‘slicerGenericScene.mrml’

http://www.na-mic.org/Wiki/index.php/Image:SlicerGenericScene.mrml

If you don’t have the FreeSurfer tutorial dataset known as ‘bert’ on your computer, then download the archive below:

http://www.na-mic.org/Wiki/index.php/Image:FreeSurferData.tar.gz


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Brain volumes . . . . . . . . . . . . . . . . . . . . . . . . .

ASEG volumes . . . . . . . . . . . . . . . . . . . . . . . . . . .

Surfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Parcellation Maps . . . . . . . . . . . . . . . . . . . . . . . . . . . .

All of the above, via a scene file. . . . . . . . . . . . . . .

Overview

From FreeSurfer, Slicer3 can load:


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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



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Loading a Brain File . .

FreeSurfer pipeline

Intensity corrected

T1 volume

Skull Stripping and Noise Filtering

Watershed Algorithm

brain.mgz


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Loading a Brain File . .

Select Volumes from the Module menu


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Loading a Brain File . .

Click on Select Volume File


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Loading a Brain File . .

Browse to find the dataset brain.mgz located in the directory

/subjects/bert/mri/

and click on Open


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Loading a Brain File . .

Choose Image Origin: Centered and click Apply


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Loading a Brain File . .

The volume brain.mgz appears in the Slice Viewer


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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


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Loading a Brain File . .

The three anatomical slices appear in the 3D Viewer


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Loading an ASEG File . .

FreeSurfer pipeline

Intensity corrected

T1 volume

Subcortical processing

Segmentation

aseg.mgz


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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 clickon Open


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Loading an ASEG File . .

Select Label Map and click on Apply


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Loading an ASEG File . .

The volume aseg.mgz appears in the Viewer

The labels are superimposed on the gray brain images


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Overlay Brain & Segmentation . .

Mouse over the labels in the Axial view


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Overlay Brain & Segmentation . .

Overlay Brain & Segmentation

The names of the labels appear in the window


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Overlay Brain & Segmentation . .

Find the labels corresponding to the Left Thalamus Proper, the Left Caudate, and the Left Putamen in the three anatomical views


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Overlay Brain & Segmentation . .

Left Thalamus Proper = #10

Left Putamen = #12

Left Caudate = #11


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Part 2: Building . .

3D Models


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Building 3D Models . .

• Building a Single Model

• Building Multiple Models


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Building a Single Model . .

Select the module Model Maker from the category Model Generation


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Building a Single Model . .

Choose Input Volume: aseg.mgz

Select Models: Create New ModelHierarchy


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Building a Single Model . .

Type in label #53, which corresponds to the label for the Right Hippocampus

Click on Apply


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Building a Single Model . .

The 3-dimensional model of the Right Hippocampus appears in the 3D Viewer


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Building 3D Models . .

• Building a Single Model

• Building Multiple Models


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Building Multiple Models . .

Delete label #53, and set the Start Label to label #10, which corresponds to theLeft Thalamus Proper

Set the End Label to label #13, which corresponds to the Left Pallidum

Check Joint Smoothing and click on Apply


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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



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Building Multiple Models Parcellation Maps

Select the module Models from the Module menu


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Loading Surfaces Parcellation Maps

Click on Load Model, and browse to find the surface lh.white located in the directory

/subjects/bert/surf/

Click on Open


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Loading Surfaces Parcellation Maps

The surface of the White Matter of the Left Hemisphere appears in the 3D Viewer


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Visualizing Parcellation Maps Parcellation Maps

Expand the tab Hierarchy & Display

and select the surface

lh.white under the tab ModelDisplay


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Visualizing Parcellation Maps 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


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Visualizing Parcellation Maps Parcellation Maps

The Parcellation Map is overlaid on the White Matter surface in the 3D Viewer



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Loading a Generic Scene File Parcellation Maps

Click on Close Scene in the File menu to close the current scene

Click OK to confirm


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Loading a Generic Scene File Parcellation Maps

• 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.


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Loading a Generic Scene File Parcellation Maps

Copy the file slicerGenericScene.mrml into the directory /subjects/ of our tutorial dataset.

/subjects/


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Loading a Generic Scene File Parcellation Maps

Copy the file slicerGenericScene.mrml located in the directory /subjects/, into the directory /subjects/bert/ of our sample subject.

/subjects/bert/


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Loading a Generic Scene File Parcellation Maps

Rename the file ‘slicerGenericScene.mrml’ located in the directory /subjects/bert/ ‘slicerBertScene.mrml’

/subjects/bert/


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Loading a Generic Scene File Parcellation Maps

Click on Load Scene in the File menu, and select the scene

slicerBertScene.mrml located in the directory /subjects/bert/


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Loading a Generic Scene File Parcellation Maps

The scene appears with a list of files which have been automatically loaded from the subject directory bert.


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Loading a Generic Scene File Parcellation Maps

Select the mode 3D only layout from the Viewer menu


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Loading a Generic Scene File Parcellation Maps

Select the module Models, and expand the tab Hierarchy & Display to display the list of models that were loaded


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Loading a Generic Scene File Parcellation Maps

Select the surface lh_pial, and turn on the visibility of the model


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Loading a Generic Scene File Parcellation Maps

Slicer displays the left hemisphere pial surface in the 3D viewer


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Loading a Generic Scene File Parcellation Maps

  • 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


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Loading a Generic Scene File Parcellation Maps

Click on the restore snapshots icon, select the snapshot Left and right white sulc, and click on restore


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Loading a Generic Scene File Parcellation Maps

The snapshot displays the left and right sulci using the GreenRed colorscheme.


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Brain volumes . . . . . . . . . . . . . . . . . . . . . . . . .

ASEG volumes . . . . . . . . . . . . . . . . . . . . . . . . . . .

Surfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Parcellation Maps . . . . . . . . . . . . . . . . . . . . . . . . . . . .

All of the above, via a scene file. . . . . . . . . . . . . . .

Summary

From FreeSurfer, Slicer3 can load:


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Conclusion . .

• 3D visualization of brain segmented surfaces and parcellation maps

• Intuitive graphical user interface to interact with FreeSurfer data

• Multi platforms open-source environment

spujol@bwh.harvard.edu