3 D Visualization of Free Surfer Data Sonia

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3 D Visualization of Free. Surfer Data Sonia Pujol, Ph. D. Silas Mann, B.

3 D Visualization of Free. Surfer Data Sonia Pujol, Ph. D. Silas Mann, B. Sc. Randy Gollub, MD. , Ph. D. Surgical Planning Laboratory Athinoula A. Martinos Center Harvard University Pujol S et al. National Alliance for Medical Image Computing -1 -

Acknowledgements National Alliance for Medical Image Computing NIH U 54 EB 005149 Neuroimage Analysis

Acknowledgements National Alliance for Medical Image Computing NIH U 54 EB 005149 Neuroimage Analysis Center NIH P 41 RR 013218 Morphometry Biomedical Informatics Research Network NIH U 24 RRO 21382 Surgical Planning Laboratory (BWH) Thanks to Nicole Aucoin Center for Functional Neuroimaging Technology NIH P 41 RR 14075 Pujol S et al. National Alliance for Medical Image Computing -2 -

Learning Objective Guide you step-by-step through the process of loading and viewing Free. Surfer

Learning Objective Guide you step-by-step through the process of loading and viewing Free. Surfer segmentations, surface reconstructions, and parcellation results within Slicer 3. Pujol S et al. National Alliance for Medical Image Computing -3 -

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

Prerequisites This tutorial assumes that you have completed the course Data Loading and Visualization. Tutorials for Slicer 3 are available on the Slicer 101 page: http: //www. na-mic. org/Wiki/index. php/Slicer 3. 2: Training Pujol S et al. National Alliance for Medical Image Computing -4 -

Prerequisites This tutorial assumes a working knowledge of how to use Free. Surfer to

Prerequisites This tutorial assumes a working knowledge of how to use Free. Surfer to generate segmentation and surface files. Tutorials for Free. Surfer are available at the following location: http: //surfer. nmr. mgh. harvard. edu/fswiki/Tutorials/ Pujol S et al. National Alliance for Medical Image Computing -5 -

Materials This tutorial requires the installation of the Slicer 3 software and the tutorial

Materials This tutorial requires the installation of the Slicer 3 software and the tutorial dataset. These materials are available at the following locations: • Slicer 3 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. Pujol S et al. National Alliance for Medical Image Computing -6 -

Materials This tutorial makes use of the same T 1 weighted image dataset (bert)

Materials This tutorial makes use of the same T 1 weighted image dataset (bert) that is used for the Free. Surfer tutorial available at the following location: http: //surfer. nmr. mgh. harvard. edu/fswiki/Fs. Tutorial If you already have the Free. Surfer subject ‘bert’ on your computer, then just download the file ‘slicer. Generic. Scene. mrml’ http: //www. na-mic. org/Wiki/index. php/Image: Slicer. Generic. Scene. mrml If you don’t have the Free. Surfer tutorial dataset known as ‘bert’ on your computer, then download the archive below: http: //www. na-mic. org/Wiki/index. php/Image: Free. Surfer. Data. tar. gz Pujol S et al. National Alliance for Medical Image Computing -7 -

Overview From Free. Surfer, Slicer 3 can load: • Brain volumes. . . •

Overview From Free. Surfer, Slicer 3 can load: • Brain volumes. . . • ASEG volumes. . . . • Surfaces. . . . • Parcellation Maps. . . . • All of the above, via a scene file. . . . Pujol S et al. National Alliance for Medical Image Computing -8 -

Overview • Part 1: Loading and Visualizing Free. Surfer Volumes • Part 2: Building

Overview • Part 1: Loading and Visualizing Free. Surfer Volumes • Part 2: Building 3 D Models • Part 3: Loading Free. Surfer Surfaces and Visualizing Parcellation Maps • Part 4: Automatic Data Loading via a Generic Scene File Pujol S et al. National Alliance for Medical Image Computing -9 -

Part 1: Loading and Visualizing Free. Surfer Volumes Pujol S et al. National Alliance

Part 1: Loading and Visualizing Free. Surfer Volumes Pujol S et al. National Alliance for Medical Image Computing -10 -

Loading a Brain File Free. Surfer pipeline Intensity corrected T 1 volume Skull Stripping

Loading a Brain File Free. Surfer pipeline Intensity corrected T 1 volume Skull Stripping and Noise Filtering Watershed Algorithm brain. mgz Pujol S et al. National Alliance for Medical Image Computing -11 -

Loading a Brain File Select Volumes from the Module menu Pujol S et al.

Loading a Brain File Select Volumes from the Module menu Pujol S et al. National Alliance for Medical Image Computing -12 -

Loading a Brain File Click on Select Volume File Pujol S et al. National

Loading a Brain File Click on Select Volume File Pujol S et al. National Alliance for Medical Image Computing -13 -

Loading a Brain File Browse to find the dataset brain. mgz located in the

Loading a Brain File Browse to find the dataset brain. mgz located in the directory /subjects/bert/mri/ and click on Open Pujol S et al. National Alliance for Medical Image Computing -14 -

Loading a Brain File Choose Image Origin: Centered and click Apply Pujol S et

Loading a Brain File Choose Image Origin: Centered and click Apply Pujol S et al. National Alliance for Medical Image Computing -15 -

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

Loading a Brain File The volume brain. mgz appears in the Slice Viewer Pujol S et al. National Alliance for Medical Image Computing -16 -

Loading a Brain File link to Click on the links icon three anatomical slices.

Loading a Brain File link to Click on the links icon three anatomical slices. Click on the Slice Visibility icon to display the slices in the 3 D Viewer Pujol S et al. National Alliance for Medical Image Computing -17 -

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

Loading a Brain File The three anatomical slices appear in the 3 D Viewer Pujol S et al. National Alliance for Medical Image Computing -18 -

Loading an ASEG File Free. Surfer pipeline Intensity corrected T 1 volume Subcortical processing

Loading an ASEG File Free. Surfer pipeline Intensity corrected T 1 volume Subcortical processing Segmentation aseg. mgz Pujol S et al. National Alliance for Medical Image Computing -19 -

Loading an ASEG File Pujol S et al. National Alliance for Medical Image Computing

Loading an ASEG File Pujol S et al. National Alliance for Medical Image Computing Click on Select Volume File, and browse to find the dataset aseg. mgz located in the directory /subjects/bert/mri/ and click on Open -20 -

Loading an ASEG File Select Label Map and click on Apply Pujol S et

Loading an ASEG File Select Label Map and click on Apply Pujol S et al. National Alliance for Medical Image Computing -21 -

Loading an ASEG File The volume aseg. mgz appears in the Viewer The labels

Loading an ASEG File The volume aseg. mgz appears in the Viewer The labels are superimposed on the gray brain images Pujol S et al. National Alliance for Medical Image Computing -22 -

Overlay Brain & Segmentation Mouse over the labels in the Axial view Pujol S

Overlay Brain & Segmentation Mouse over the labels in the Axial view Pujol S et al. National Alliance for Medical Image Computing -23 -

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

Overlay Brain & Segmentation The names of the labels appear in the window Pujol S et al. National Alliance for Medical Image Computing -24 -

Overlay Brain & Segmentation Find the labels corresponding to the Left Thalamus Proper, the

Overlay Brain & Segmentation Find the labels corresponding to the Left Thalamus Proper, the Left Caudate, and the Left Putamen in the three anatomical views Pujol S et al. National Alliance for Medical Image Computing -25 -

Overlay Brain & Segmentation Left Thalamus Proper = #10 Left Putamen = #12 Left

Overlay Brain & Segmentation Left Thalamus Proper = #10 Left Putamen = #12 Left Caudate = #11 Pujol S et al. National Alliance for Medical Image Computing -26 -

Part 2: Building 3 D Models Pujol S et al. National Alliance for Medical

Part 2: Building 3 D Models Pujol S et al. National Alliance for Medical Image Computing -27 -

Building 3 D Models • Building a Single Model • Building Multiple Models Pujol

Building 3 D Models • Building a Single Model • Building Multiple Models Pujol S et al. National Alliance for Medical Image Computing -28 -

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

Building a Single Model Select the module Model Maker from the category Model Generation Pujol S et al. National Alliance for Medical Image Computing -29 -

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

Building a Single Model Choose Input Volume: aseg. mgz Select Models: Create New Model. Hierarchy Pujol S et al. National Alliance for Medical Image Computing -30 -

Building a Single Model Type in label #53, which corresponds to the label for

Building a Single Model Type in label #53, which corresponds to the label for the Right Hippocampus Click on Apply Pujol S et al. National Alliance for Medical Image Computing -31 -

Building a Single Model The 3 -dimensional model of the Right Hippocampus appears in

Building a Single Model The 3 -dimensional model of the Right Hippocampus appears in the 3 D Viewer Pujol S et al. National Alliance for Medical Image Computing -32 -

Building 3 D Models • Building a Single Model • Building Multiple Models Pujol

Building 3 D Models • Building a Single Model • Building Multiple Models Pujol S et al. National Alliance for Medical Image Computing -33 -

Building Multiple Models Delete label #53, and set the Start Label to label #10,

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 Pujol S et al. National Alliance for Medical Image Computing -34 -

Building Multiple Models The 3 -dimensional models of the Left Thalamus Proper (label #10),

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 3 D Viewer Pujol S et al. National Alliance for Medical Image Computing -35 -

Part 3: Loading Free. Surfer Surfaces and Visualizing Parcellation Maps Pujol S et al.

Part 3: Loading Free. Surfer Surfaces and Visualizing Parcellation Maps Pujol S et al. National Alliance for Medical Image Computing -36 -

Building Multiple Models Select the module Models from the Module menu Pujol S et

Building Multiple Models Select the module Models from the Module menu Pujol S et al. National Alliance for Medical Image Computing -37 -

Loading Surfaces Click on Load Model, and browse to find the surface lh. white

Loading Surfaces Click on Load Model, and browse to find the surface lh. white located in the directory /subjects/bert/surf/ Click on Open Pujol S et al. National Alliance for Medical Image Computing -38 -

Loading Surfaces The surface of the White Matter of the Left Hemisphere appears in

Loading Surfaces The surface of the White Matter of the Left Hemisphere appears in the 3 D Viewer Pujol S et al. National Alliance for Medical Image Computing -39 -

Visualizing Parcellation Maps Expand the tab Hierarchy & Display and select the surface lh.

Visualizing Parcellation Maps Expand the tab Hierarchy & Display and select the surface lh. white under the tab Model. Display Pujol S et al. National Alliance for Medical Image Computing -40 -

Visualizing Parcellation Maps Click on Load Free. Surfer Overlay, browse to find the Parcellation

Visualizing Parcellation Maps Click on Load Free. Surfer Overlay, browse to find the Parcellation Map lh. aparc. annot located in the directory /subjects/bert/label/ Pujol S et al. and click on Open National Alliance for Medical Image Computing -41 -

Visualizing Parcellation Maps The Parcellation Map is overlaid on the White Matter surface in

Visualizing Parcellation Maps The Parcellation Map is overlaid on the White Matter surface in the 3 D Viewer Pujol S et al. National Alliance for Medical Image Computing -42 -

Part 4: Automatic Data Loading via a Generic Scene File Pujol S et al.

Part 4: Automatic Data Loading via a Generic Scene File Pujol S et al. National Alliance for Medical Image Computing -43 -

Loading a Generic Scene File Click on Close Scene in the File menu to

Loading a Generic Scene File Click on Close Scene in the File menu to close the current scene Click OK to confirm Pujol S et al. National Alliance for Medical Image Computing -44 -

Loading a Generic Scene File • The generic scene file works by looking in

Loading a Generic Scene File • The generic scene file works by looking in the subject directory created by Free. Surfer, and loading all available volumes and models based on known subdirectory names and filenames. • The file slicer. Generic. Scene. mrml will work properly if the subdirectory names and filenames have not been changed by the user. Pujol S et al. National Alliance for Medical Image Computing -45 -

Loading a Generic Scene File Copy the file slicer. Generic. Scene. mrml into the

Loading a Generic Scene File Copy the file slicer. Generic. Scene. mrml into the directory /subjects/ of our tutorial dataset. /subjects/ Pujol S et al. National Alliance for Medical Image Computing -46 -

Loading a Generic Scene File Copy the file slicer. Generic. Scene. mrml located in

Loading a Generic Scene File Copy the file slicer. Generic. Scene. mrml located in the directory /subjects/, into the directory /subjects/bert/ of our sample subject. /subjects/bert/ Pujol S et al. National Alliance for Medical Image Computing -47 -

Loading a Generic Scene File Rename the file ‘slicer. Generic. Scene. mrml’ located in

Loading a Generic Scene File Rename the file ‘slicer. Generic. Scene. mrml’ located in the directory /subjects/bert/ ‘slicer. Bert. Scene. mrml’ /subjects/bert/ Pujol S et al. National Alliance for Medical Image Computing -48 -

Loading a Generic Scene File Click on Load Scene in the File menu, and

Loading a Generic Scene File Click on Load Scene in the File menu, and select the scene slicer. Bert. Scene. mrml located in the directory /subjects/bert/ Pujol S et al. National Alliance for Medical Image Computing -49 -

Loading a Generic Scene File The scene appears with a list of files which

Loading a Generic Scene File The scene appears with a list of files which have been automatically loaded from the subject directory bert. Pujol S et al. National Alliance for Medical Image Computing -50 -

Loading a Generic Scene File Select the mode 3 D only layout from the

Loading a Generic Scene File Select the mode 3 D only layout from the Viewer menu Pujol S et al. National Alliance for Medical Image Computing -51 -

Loading a Generic Scene File Select the module Models, and expand the tab Hierarchy

Loading a Generic Scene File Select the module Models, and expand the tab Hierarchy & Display to display the list of models that were loaded Pujol S et al. National Alliance for Medical Image Computing -52 -

Loading a Generic Scene File Select the surface lh_pial, and turn on the visibility

Loading a Generic Scene File Select the surface lh_pial, and turn on the visibility of the model Pujol S et al. National Alliance for Medical Image Computing -53 -

Loading a Generic Scene File Slicer displays the left hemisphere pial surface in the

Loading a Generic Scene File Slicer displays the left hemisphere pial surface in the 3 D viewer Pujol S et al. National Alliance for Medical Image Computing -54 -

Loading a Generic Scene File The generic scene includes three snapshots that provide a

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 Pujol S et al. National Alliance for Medical Image Computing -55 -

Loading a Generic Scene File Click on the restore snapshots icon, select the snapshot

Loading a Generic Scene File Click on the restore snapshots icon, select the snapshot Left and right white sulc, and click on restore Pujol S et al. National Alliance for Medical Image Computing -56 -

Loading a Generic Scene File The snapshot displays the left and right sulci using

Loading a Generic Scene File The snapshot displays the left and right sulci using the Green. Red colorscheme. Pujol S et al. National Alliance for Medical Image Computing -57 -

Summary From Free. Surfer, Slicer 3 can load: • Brain volumes. . . •

Summary From Free. Surfer, Slicer 3 can load: • Brain volumes. . . • ASEG volumes. . . . • Surfaces. . . . • Parcellation Maps. . . . • All of the above, via a scene file. . . . Pujol S et al. National Alliance for Medical Image Computing -58 -

Conclusion • 3 D visualization of brain segmented surfaces and parcellation maps • Intuitive

Conclusion • 3 D visualization of brain segmented surfaces and parcellation maps • Intuitive graphical user interface to interact with Free. Surfer data • Multi platforms open-source environment [email protected] harvard. edu Pujol S et al. National Alliance for Medical Image Computing -59 -